Detection of mecA variant strains of methicillin-resistant Staphylococcus aureus

ABSTRACT

The present invention provides improved tests for the detection of methicillin-resistant  Staphylococcus aureus  bearing a variant mecA gene. The tests are particularly useful for eliminating certain false negative results due to the presence of this variant in MRSA in patient samples.

STATEMENT OF PRIORITY

This application claims priority to European Patent Application No. EP11306776.3, filed Dec. 23, 2011, the entire contents of which are incorporated by reference herein.

FIELD OF THE INVENTION

The present invention relates to molecular detection of methicillin-resistant Staphylococcus aureus (MRSA). More particularly, the present invention relates to an improved detection of MRSA that includes additional strains bearing a variant of the mecA gene.

BACKGROUND OF THE INVENTION

A strain of Staphylococcus aureus was shown for the first time in 1961 to be resistant to methicillin. Today, methicillin-resistant Staphylococcus aureus (MRSA) is one of the most prevalent antibiotic resistance pathogen causing hospital and community infections. The emergence of MRSA strains is due to the acquisition and insertion of a mobile genetic element, the Staphylococcal Cassette Chromosome mec (SCCmec), into the chromosome of susceptible S. aureus strains. Indeed, this SCCmec element carries the mecA gene, which is responsible for methicillin resistance (Staphylococcal Cassette Chromosome mec; Ito et al., 2001, Antimicrob. Agents Chemother. 45(5):1323-1336; Hiramatsu, et al., 2001, Trends Microbiol. October; 9(10):486-93). The mecA gene encodes for a modified Penicillin Binding Protein called PBP2a or PBP2′. Contrary to the native PBP, this PBP2a has a low affinity for the β-lactam antibiotics that permits to continue the synthesis of cell wall even in presence of β-lactam antibiotics.

SCCmec element can be incorporated into the chromosome of S. aureus and other coagulase negative Staphylococci, mainly S. epidermidis and S. haemolyticus. SCCmec is characterized by the presence of terminal inverted and direct repeats, a set of site-specific recombinase genes (ccrA and ccrB), and the mecA gene complex (Ito et al., 1999, Antimicrob. Agents Chemother, 43:1449-1458; Katayama et al., 2000, Antimicrob. Agents Chemother. 44:1549-1555). The site of insertion of this mecA gene cassette SCCmec into the Staphylococcus aureus genome is known and the sequence conserved (Ito et al., 2001, Antimicrob. Agents Chemother. 45:1323-1336). After insertion into the S. aureus chromosome, the SCCmec has a left extremity junction and a right extremity junction (see FIG. 1), with a surrounding left extremity junction region and right extremity junction region, respectively, that includes the SCCmec cassette and chromsosomal DNA where the SCCmec sequence is contiguous with the S. aureus chromosomal sequence. The nucleotide sequence of the regions surrounding the left and right boundaries of SCCmec DNA (i.e., attL and attR, respectively), as well as those of the regions around the SCCmec DNA integration site (i.e., attBscc, the bacterial chromosome attachment site for SCCmec DNA), have previously been analyzed. Sequence analysis of the integration sites revealed that attBscc is located at the 3′ end of a novel open reading frame (ORF), orfX. orfX encodes a polypeptide of 159 amino acids annotated recently as a 23S rRNA methyltransferase (www.uniprot.org/uniprot/Q6I7F2). Organization of the mecA region of SCCmec has additionally been studied (Oliveira et al., 2000, Antimicrob. Agents Chemother. 44(7):1906-1910).

Typically, in an MRSA assay in a patient, a nasal swab is taken from the patient and cultured repeatedly, to determine if an MRSA strain is present. Newer methods are being developed that allow identification of MRSA directly from a nasal swab and in a much shorter amount time. Samples are also evolving, and many papers show the interest to sample several anatomical sites of the same patient to increase the possibility to detect MRSA carriers. The sites could be nasal plus throat, axilla, groin and or perineum. (Methicillin Resistant Staphylococcus aureus colonisation at different Body Sites: a Prospective, Quantitative Analysis, Mermel et al. 2011, Journal of Clinical Microbiology).

Amplification is a well known art, and various methods have been developed, including transcription-based amplification such as transcription-mediated amplification (TMA; U.S. Pat. Nos. 5,766,849 5,399,491; 5,480,784; 5,766,849; and 5,654,142) and nucleic acid sequence-based amplification (NASBA; U.S. Pat. Nos. 5,130,238; 5,409,818; 5,654,142; and 6,312,928), and cycling nucleic acid amplification technologies (thermocycling) such as polymerase chain reaction (PCR; U.S. Pat. Nos. 4,683,195; 4,965,188; 4,683,202) and ligase chain reaction (LCR; U.S. Pat. No. 5,792,607). Known amplification methods also include strand displacement amplification (SDA), self-sustained sequence replication (3SR), Q-β replicase, and cascade rolling circle amplification (CRCA).

Detection methods utilizing nucleic acids are also well known in the art. Nucleic acids are often labeled for various detection purposes. For example, methods described in U.S. Pat. Nos. 4,486,539 (Kourlisky); 4,411,955 (Ward); 4,882,269 (Schneider) and 4,213,893 (Carrico), illustrate preparation of labeled detection probes for detecting specific nucleic acid sequences. Probe designs for different detection methods, such as target-capture, HPA, TaqMan, molecular beacons and sandwich hybridization have also been described (e.g., U.S. Pat. No. 4,486,539, and U.S. Pat. Nos. 4,751,177; 5,210,015; 5,487,972; 5,804,375; 5,994,076). Nucleic acid hybridization techniques and conditions are known to the skilled artisan and have been described for example, in Sambrook et al. Molecular Cloning A Laboratory Manual, 2nd Ed. Cold Spring Lab. Press, December 1989; U.S. Pat. Nos. 4,563,419 (Ranki) and 4,851,330 (Kohne) and in Dunn, et al., Cell 12, pp. 23-26 (1978) among many other publications.

Earlier molecular methods developed to detect and identify MRSA based on the detection of the mecA gene and S. aureus-specific chromosomal sequences have been described. (Saito et al., 1995, J. Clin. Microbiol. 33:2498-2500; Ubukata et al., 1992, J. Clin. Microbiol. 30:1728-1733; Murakami et al., 1991, J. Clin. Microbiol. 29:2240-2244; Hiramatsu et al., 1992, Microbiol. Immunol. 36:445-453). However, in tests based on the detection of the cassette junction only, false positives have been observed with methicillin-susceptible S. aureus isolates containing a small fragment of the right extremity of the SCCmec (see Rupp, J. et al., J. Clin. Microbiol. 44(6): 2317 (2006)). Additionally, Ramakrishnan and Riccelli describe a method for detecting MRSA utilizing oligonucleotide probes having sequences that are complementary to regions near the left junction of the SCCmec cassette insertion site, including part of the SCCmec cassette sequence and part of the S. aureus sequence in the region of insertion (the left extremity junction region) (U.S. patent publication No. US20060057613).

Concepts for determining resistance to methicillin carried specifically by S. aureus have been published:

-   -   the SCCmec right extremity junction amplification concept         (Hiramatsu et al. WO97/31125; EP 0 887 424; U.S. Pat. No.         6,156,507; and further, Huletsky and Rossbach WO02/099034         (2002); Huletsky et al. J. Clin. Microbiol. 42(5): 1875-1884         (2004))     -   the immuno-enrichment concept described by François and         co-workers (Francois, P et al, J. Clin. Microbiol. 41(1):254-260         (2003); WO02082086), in which the immuno-enrichment is followed         by amplification of three markers (mecA gene, S. aureus-specific         marker, and S. epidermidis-specific marker)     -   the combination of SCCmec right extremity junction amplification         and mecA amplification (Jay, et al. US20090203013; WO2009085221,         which are incorporated by reference in their entirety).

The SCCmec right extremity junction concept is based on the amplification of a region covering the right extremity junction region of the SCCmec integration site. The principle is the following: the SCCmec cassette always integrates the S. aureus chromosome upstream of a S. aureus specific open reading frame called orfX; the amplification (e.g., PCR) assay combines multiple forward primers located on the right part of the cassette (“right extremity junction region” of SCCmec cassette), one reverse primer and a probe, both located in the S. aureus chromosomal orfX, i.e., downstream of the right extremity junction of SCCmec with orfX (“right extremity junction region” of orfX). Hiramatsu et al. describe a test with two forward primers in the right extremity junction region of the cassette to amplify the main SCCmec types described at that time (one primer for SCCmec types I and II and a second primer for type III). Huletsky et al set forth that several MRSA strains were not detected if only the two forward primers described by Hiramatsu were used, and they determined new types of cassettes named as MREJ types having sequence variations in the right part of the SCCmec cassette. A commercially available (Infectio Diagnostics Inc.) test combines five forward primers located in the right part of the cassette (one primer was designed for the detection of MREJ types i and ii and the four others for the MREJ types iii, iv, v and vii), one reverse primer located in the orfX, and three generic probes covering the same portion of the orfX region and required to identify the orfX variants identified. This test is performed in real-time PCR. However, the specificity of this test as reported (Huletsky et al. 2004) shows that 4.6% of MSSA (26 out of 569 tested) were misidentified. False-positive result has also been reported with another commercial test using a single-locus (right extremity SCCmec cassette-orfX junction) PCR assay (Rupp et al. J. Clin. Microbiol. (44)6: 2317 (2006)).

US20090203013 addressed primary sources of MRSA false positives and provided an improved test to detect MRSA that had not been previously addressed by then-available tests. This application provided that the identification of false positives by the previous molecular methods can be explained in some instances by the presence in MSSA strains of a residual SCCmec right extremity fragment following the deletion of a chromosomal region containing mecA or the presence of an SCCmec which does not contain mecA. Additionally, it provided that some portion of the false positives can be due to non specific amplification; indeed, because the reverse primer and the probes are located in the orfX which is common to both MRSA and MSSA, non specific annealing of the forward primer(s) on MSSA chromosome will lead to amplification and detection of MSSA. The application addressed both sources of false positives and provided an improved test. An assay utilizing this principle is marketed (NucliSENS EasyQ® MRSA, bioMérieux, SA, Marcy l'Etoile, France).

Previously, in assays for detection of methicillin resistance in S. aureus, either the mecA gene was determined to be present in the SCCmec cassette leading the strain to be resistant to methicillin or the mecA gene was determined to be absent (excision from the cassette or no cassette) wherein it was concluded that the strain was susceptible to methicillin. Taking into account the numerous sequences available in public databanks for mecA gene, from MRSA or from other methicillin-resistance pathogens, the mecA gene was shown as well-conserved, only some particular mutations were found.

Recently a methicillin-resistant S. aureus was detected that was found to lack mecA by conventional PCR and microarray sequencing (Shore et al., Antimicrob. Agents Chemother. Doi:10.1128/AAC.00187-11 (2 Jun. 2011) and Garcia-Alvarez, L. et al., Lancet doi:10.1016/S1473-3099(11)70126-8 (3 Jun. 2011) Methicillin-resistant Staphylococcus aureus with a novel mecA homologue in human and bovine population in the UK and Denmark: a descriptive study.). Whole-genome sequencing revealed a 30 kb SCCmec element having a highly divergent blaZ-mecA-mecRI-mecI, and indicated that the mec element present in the SCCmec element had 70% sequence identity to S. aureus mecA homologues; further, the SCCmec element was almost identical to SCCmec type XI previously identified (sequence type 425 bovine MRSA strain LGA251 listed on the website of the International Working Group on the Classification of Staphylococcal Cassette Chromosome Elements). The SCCmec element is integrated at the same nucleotide position within orfX as all other SCCmec elements. The strain additionally included a class E mec complex a type 8 cassette chromosome recombinase (ccr) complex consisting of ccrA1-ccrB3, an arsenic resistance operon and flanking direct repeats. Present detection methods would not identify this strain as MRSA.

Shore et al. used the FR823292 strain as reference strain and used mecA_M10/0061 primers. Garcia-Alvarez et al. studied a divergent mecA in the LGA251 genome, this mecA variant being located in a novel cassette designated “type-XI SCCmec.” They used the LGA251 strain as reference strain and used mecA_LGA251 primers. In fact, the 2 publications refer to the same subject. Both mecA variants shared a very high similarity percentage (99%) and in the same time show a weak overall similarity to all mecA sequences known so far.

As new subtypes and strains are identified, means to detect such subtypes and strains becomes necessary. This is particularly important when a currently existing assay does not fortuitously already detect it and thus can result in false negative results. The present invention fills this need regarding detection of strains containing variant mecA by providing an assay that can detect such strains. Further, this new invention confirms in the same assay the presence of both a S. aureus strain and a methicillin-resistance gene. This assay can be used alone or in combination with existing assays for other SCCmec types.

SUMMARY OF THE INVENTION

The present invention provides a method of amplifying in a sample a methicillin-resistant Staphylococcus aureus (MRSA) which comprises an insertion of an SCCmec cassette within Staphylococcus aureus chromosomal DNA, wherein the SCCmec cassette comprises a mecA variant element, the method comprising:

performing on the sample an amplification reaction utilizing an oligonucleotide set comprising:

a. a first oligonucleotide having a nucleic acid sequence capable of specifically hybridizing to a region of chromosomal Staphylococcus aureus DNA in an extremity junction region, and

b. a second oligonucleotide having a nucleic acid sequence capable of specifically hybridizing to a region of a mecA variant, wherein each of the first oligonucleotide and the second oligonucleotide is oriented such that, under amplification conditions, if the sample contains the MRSA, the region of the MRSA between the hybridizing region of the first oligonucleotide and the hybridizing region of the second oligonucleotide is amplified.

The present invention additionally provides a method of amplifying in a sample a methicillin-resistant Staphylococcus aureus (MRSA) which comprises an insertion of an SCCmec cassette within Staphylococcus aureus chromosomal DNA, wherein the SCCmec cassette comprises mecA or a mecA variant element, the method comprising: performing on the sample an amplification reaction utilizing

a. a first oligonucleotide set comprising:

-   -   1) a first mecA variant oligonucleotide having a nucleic acid         sequence capable of specifically hybridizing to a first region         of a mecA variant element, and     -   2) a second mecA variant oligonucleotide having a nucleic acid         sequence capable of specifically hybridizing to a second region         of a mecA variant element; and

b. a second oligonucleotide set comprising:

-   -   1) a first mecA oligonucleotide having a nucleic acid sequence         capable of specifically hybridizing to a first region of mecA,         and     -   2) a second mecA oligonucleotide having a nucleic acid sequence         capable of specifically hybridizing to a second region of mecA         wherein each of the first oligonucleotide and the second         oligonucleotide is oriented such that, under amplification         conditions, if the sample contains the MRSA, the region of the         MRSA between the hybridizing region of the first oligonucleotide         and the hybridizing region of the second oligonucleotide is         amplified.

The present invention further provides a kit for amplifying a methicillin-resistant Staphylococcus aureus (MRSA) which comprises an insertion of an SCCmec cassette within Staphylococcus aureus chromosomal DNA, wherein the SCCmec cassette comprises a mecA variant element, the kit comprising a first oligonucleotide set comprising:

a. a first oligonucleotide having a nucleic acid sequence capable of specifically hybridizing to a region of chromosomal Staphylococcus aureus DNA in an extremity junction region, and

b. a second oligonucleotide having a nucleic acid sequence capable of specifically hybridizing to a region of a mecA variant.

Additionally, the present invention provides a kit for amplifying in a sample a methicillin-resistant Staphylococcus aureus (MRSA) which comprises an insertion of an SCCmec cassette within Staphylococcus aureus chromosomal DNA, wherein the SCCmec cassette comprises mecA or a mecA variant element, the kit comprising:

a) a first oligonucleotide set comprising:

-   -   1) a first mecA variant oligonucleotide having a nucleic acid         sequence capable of specifically hybridizing to a first region         of a mecA variant element, and     -   2) a second mecA variant oligonucleotide having a nucleic acid         sequence capable of specifically hybridizing to a second region         of a mecA variant element; and

b) a second oligonucleotide set comprising:

-   -   1) a first mecA oligonucleotide having a nucleic acid sequence         capable of specifically hybridizing to a first region of mecA,         and     -   2) a second mecA oligonucleotide having a nucleic acid sequence         capable of specifically hybridizing to a second region of mecA.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 shows the region of MRSA chromosome with the inserted SSCmec cassette, indicating the left and right extremity junctions.

FIG. 2 shows the region of MRSA chromosome with an inserted SCCmec cassette bearing a mecA variant (mecA_(LGA251)).

DETAILED DESCRIPTION OF THE INVENTION

As discussed herein, the present invention provides the identification of strains of methicillin-resistant S. aureus which include a variant mecA gene (typically not detected with presently commercially-available MRSA detection kits) and which are structurally arranged such that a single amplification reaction can amplify both a relevant portion of mecA and an extremity junction at the insertion point of a SCCmec cassette into the S. aureus chromosome. The present invention addresses a newly-discovered source of false negative results and provides an improved test.

Unless defined otherwise, all technical and scientific terms used herein have the same meanings as commonly understood by one of skill in the art to which the disclosed invention belongs. Although any methods and materials similar or equivalent to those described herein can be used in the practice or testing of the present invention, the preferred methods, devices, and materials are as described.

As used herein and in the appended claims, the singular forms “a,” “an,” and “the” include plural reference unless the context clearly dictates otherwise.

The strains identified by the present invention are methicillin-resistant, but they do not harbour the classical mecA gene known to be well-conserved so far. Methicillin resistance is conferred in this case by a new mecA variant gene. One documented mecA variant is referred to in publications variously as mecA_(LGA251), mecA_(M10/0061), mecA homologue, and mecA_(new variant) (this variant has more recently been proposed to be renamed “mecC” [Ito et al. “Guidelines for Reporting Novel mecA Gene Homologues” Agents Chemother. doi:10.1128/AAC.01199-12]); however, other mecA variants may be detected with the present invention. As used in the specification and the claims, the term “mecA variant” will be used to refer to any mecA variant gene that confers methicillin resistance and can be detected by a claimed method, in particular, in an amplification reaction that, with a single primer set, amplifies a region that includes both a relevant portion of a mecA variant (i.e., sufficient to identify it as a mecA variant) and an extremity junction at the insertion point of a SCCmec cassette into the S. aureus chromosome. It is noted that, as amplification technologies are further developed, longer amplicons may become possible such that primer sets for detection of a mecA variant gene may be designed to hybridize farther from this target region comprising a relevant portion of a mecA variant gene and an extremity junction of SCCmec cassette.

The size of the SCCmec cassettes in previously studied MRSA strains is divergent, but generally the mecA gene has been found to be about 8000 to 15,000 bp from the S. aureus chromosome in the direction of orfX (sometimes herein referred to as “downstream”) and longer in the other direction (see FIG. 1 and FIG. 2a ). In the new SCCmec type XI, the mecA variant gene has been found to be positioned closer to orfX, with the distance only about 1500 bp (see FIG. 2b ). While application of traditional MRSA amplification designs might have predicted an assay design of two parts—detection of the mecA variant gene in addition to detection of the junction—applicants instead considered and recognized the potential utility of the shorter distance from mecA variant gene to orfX. Thus, the present invention advantageously amplifies the region between the mecA variant gene and an S. aureus chromosomal extremity junction region (i.e., across an extremity junction) directly using a primer in the mecA variant gene and another in the S. aureus chromosome region in an extremity junction region (see FIG. 2, e.g., across the right extremity junction). While still an unconventionally long amplicon, applicants have found that this design works surprisingly well. Additionally, this new invention resolves the problem of poor specificity because only one amplification is needed and this amplification confirms in the same reaction the presence both of S. aureus strain and of variant methicillin-resistance gene.

The present invention provides a method of amplifying in a sample a methicillin-resistant Staphylococcus aureus (MRSA) which comprises an insertion of an SCCmec cassette within Staphylococcus aureus chromosomal DNA, wherein the SCCmec cassette comprises a mecA variant element, the method comprising:

performing on the sample an amplification reaction utilizing an oligonucleotide set comprising:

a. a first oligonucleotide having a nucleic acid sequence capable of specifically hybridizing to a region of chromosomal Staphylococcus aureus DNA in an extremity junction region, and

b. a second oligonucleotide having a nucleic acid sequence capable of specifically hybridizing to a region of a mecA variant, wherein each of the first oligonucleotide and the second oligonucleotide is oriented such that, under amplification conditions, if the sample contains the MRSA, the region of the MRSA between the hybridizing region of the first oligonucleotide and the hybridizing region of the second oligonucleotide is amplified. The region of chromosomal S. aureus DNA can be in a right extremity junction region.

Oligonucleotides of the present invention that specifically hybridize with a target can be selected as those which selectively hybridize, at the selected hybridization conditions, with their target, i.e., which bind with their intended target(s) but not with non-targets. Hybridization/amplification conditions can be selected for appropriate stringency to achieve selectivity, as is known in the art (e.g., Sambrook and Russell, Molecular Cloning: A Laboratory Manual (Cold Spring Harbor Laboratory Press; 3rd edition (2001)). Minor modifications can be made to select oligonucleotides as long as the reaction conditions allow the modified oligonucleotide to specifically hybridize to the target(s).

A first oligonucleotide having a nucleic acid sequence capable of specifically hybridizing to a region of chromosomal Staphylococcus aureus DNA in an extremity junction region and a second oligonucleotide having a nucleic acid sequence capable of specifically hybridizing to a region of a mecA variant each can function as a primer, and each is oriented such that, upon hybridization to its specific target nucleic acid, and upon initiation of an amplification reaction including the primer, an amplicon is formed that includes the region of the MRSA between the hybridizing region of the first oligonucleotide and the hybridizing region of the second oligonucleotide. Such a reaction is designed to amplify across an extremity junction of SCCmec at its insertion into the S. aureus chromosome (i.e., to be in sufficiently close proximity of the junction so that an amplification reaction can extend across the junction). Thus a primer pair for mecA variant useful for amplifying a junction will typically hybridize to two regions, one in the mecA variant and one in an S. aureus chromosomal region, in effect surrounding the junction, and each primer will be oriented to hybridize such as to be capable of directing amplification in a 5′-3′ direction toward the junction. Typically, the primer for mecA variant would be designed to hybridize within 1600 nt, 1550 nt, 1500 nt, 1450 nt, 1400 nt, 1350 nt, 1300 nt, 1200 nt, 1100 nt, 1000 nt, 900 nt, 800 nt, 700 nt, 600 nt, 500 nt, 400 nt, 350 nt, 300 nt, 250 nt, 200 nt 150 nt, 100 nt, 50 nt, 30 nt, 25 nt, 20 nt, etc. of the junction; however, as new technologies allow longer amplicons, primers can be designed that hybridize farther distances from the junction. The primer having a nucleic acid sequence capable of specifically hybridizing to a region of a mecA variant will typically be designed to hybridize farther from the junction than the primer having a nucleic acid sequence capable of specifically hybridizing to a region of chromosomal Staphylococcus aureus DNA in an extremity junction region because of the organization of the SCCmec having a mecA variant gene and the distance of the mecA variant gene from the junction.

The oligonucleotide set for amplification of orfX-mecA variant can further comprise a third oligonucleotide capable of specifically hybridizing within a region of the MRSA between the hybridizing region of the first oligonucleotide and the hybridizing region of the second oligonucleotide, and, wherein if the sample contains the MRSA, hybridization of the third oligonucleotide is detected. Such an oligonucleotide can function as a probe for detecting an amplification product and is therefore selected to be capable of specifically hybridizing to a region between the hybridizing region of the first oligonucleotide and the hybridizing region of the second oligonucleotide. In certain embodiments, such a probe can specifically hybridize to a region of chromosomal Staphylococcus aureus DNA, such as a region of orfX. In another embodiment, a probe can specifically hybridize to a region of a right extremity junction region of SCCmec cassette DNA (e.g., within blaZ sequences), and in a further embodiment, a probe can specifically hybridize to a region of the mecA variant. Amplification can be detected by any means selected. For example, this third oligonucleotide can be labeled by any of several means and with any of several methods. Thus, if the sample contains the MRSA, amplification of the nucleic acid between the two primers occurs, and the third oligonucleotide, which can be a labeled probe, can hybridize to the amplicon. Hybridization of the third oligonucleotide can be detected by any known means. Alternatively, an intercalating dye can be used to detect amplification from the two primers. If a probe is used, the probe can be designed to specifically hybridize to a region of a right extremity junction region of SCCmec cassette DNA. For example, the probe can be designed to specifically hybridize to a region of chromosomal Staphylococcus aureus DNA such as a region of orfX of chromosomal Staphylococcus aureus DNA. Alternatively, a probe can be designed to specifically hybridize to a region of the mecA variant.

The presence or absence of any target within the present invention can be determined by performing whatever analysis provides detection of the product, e.g., if a labeled probe is used, detection of the hybridized label by the appropriate detection device. In such an embodiment, lack of a detectable signal indicates the absence of the target; perception of a detectable signal indicates presence of the target.

Examples of a first oligonucleotide, or primer, capable of specifically hybridizing to a region of chromosomal Staphylococcus aureus DNA in an extremity junction region can include, but are not limited to, an oligonucleotide that specifically hybridizes in the orfX region. Examples of such an oligonucleotide include SEQ ID NOs:9 and 10. Examples of a second oligonucleotide having a nucleic acid sequence capable of specifically hybridizing to a region of a mecA variant can include, but are not limited to, a nucleic acid sequence selected from the group consisting of: SEQ ID NOs:6, 7, 16, 17 and 21. These specific examples are particularly useful as forward primers (i.e., for directing amplification toward the right extremity junction of SCCmec). Examples of a third oligonucleotide, which can be used as a probe, capable of specifically hybridizing within a region of the MRSA between the hybridizing region of the first oligonucleotide (hybridizing within in chromosomal Staphylococcus aureus DNA) and the hybridizing region of the second oligonucleotide (hybridizing within a region of a mecA variant) can include, but is not limited to, a nucleic acid sequence set forth as SEQ ID NO: 8, 18 and 19.

The genomic structure of MRSA has been characterized previously. As used in the claims, the “SCCmec cassette” (sometimes referred to as “mecDNA,” e.g., in Hiramatsu U.S. Pat. No. 6,156,507) has the definition as known in the art, i.e., an integrated adventitious DNA existing on a chromosome of MRSA or MR-CNS and including the mec gene complex, a set of site-specific recombinase genes (ccrA and ccrB), and terminal inverted and direct repeats (at both 3′ and 5′ ends); as used in the specification, this term includes any variation of SCCmec found in strains harboring a mecA variant. “mecA gene” includes all sequences necessary to confer methicillin resistance (i.e., to encode PBP2a or PBP2′ (Penicillin Binding Protein)).

As known in the art, insertion of the SCCmec cassette into the S. aureus chromosome creates two junctions, and two corresponding junction regions, of SCCmec DNA with S. aureus chromosomal DNA, wherein the SCCmec sequence is contiguous with the S. aureus chromosomal sequence. The junctions, therefore, are located at the left and right extremities of the SCCmec cassette (see FIG. 1). These two regions are named “Right SCCmec-Chromosome Junction” and “Chromosome-Left SCCmec junction” by Ito et al. (Antimicrob. Agents Chemother, May 2001 45(5): 1323-1336, “Structural Comparison of three Types of Staphylococcal Cassette Chromosome mec Integrated in the chromosome in Methicillin-Resistant Staphylococcus aureus”), and termed herein as “right extremity junction” and “left extremity junction,” respectively. At the right extremity junction, the S. aureus genomic sequence abutting the SCCmec cassette is the gene orfX, which is in some literature referred to as “IntM.” As used in the claims, “extremity junction region” is a region of either SCCmec cassette or S. aureus chromosomal nucleic acid within distance of either the right or the left extremity junction, or insertion site, such that a primer that hybridizes in either SCCmec (e.g., J3 region) or orfX can, in a primer extension reaction or a transcription-type (e.g., NASBA or TMA) reaction, be extended across that junction, e.g., within 600 nt, 550 nt, 500 nt, 450 nt, 400 nt, 350 nt, 300 nt, 250 nt, 200 nt, 150 nt, 100 nt, or 50 nt (in either direction) of the junction. Useful distances may vary depending upon the amplification technology used. “Extremity junction region,” therefore, depending upon context used, can refer to a region within the SCCmec DNA or a region within the S. aureus chromosomal DNA; both uses refer to such DNA within distance of the junction such that an appropriately selected primer that hybridizes in either SCCmec (e.g., J3 region) or orfX could, under appropriate, standard extension or amplification conditions, be extended, or transcribed, from it, in the direction of the junction, across the junction. That is, “an extremity junction region of the SCCmec cassette” would be a region within the SCCmec DNA near its abutment, or integration site, with the S. aureus chromosomal DNA; and “an extremity junction region of orfX” would be a region within the orfX DNA near an abutment with SCCmec DNA (an SCCmec integration site). Similarly, “an extremity junction region of chromosomal S. aureus DNA” would be a region within the chromosomal S. aureus DNA near an abutment with SCCmec DNA. Alternatively, this region may also be referred to as chromosomal S. aureus DNA in the region of the SCCmec extremity junction. Thus, “right extremity junction region” refers to the region surrounding the junction on the right (or downstream) side of the SCCmec cassette, and “left extremity junction region” refers to the region surrounding the junction on the left (or upstream) side of the SCCmec cassette (see FIG. 1).

Advantageously, one can perform an amplification reaction to detect both the presence of previously characterized MRSA strains (containing the originally-described mecA gene), using known methods, such as one comprising detecting a SCCmec insertion junction and mecA sequences (i.e., Jay et al.), along with an amplification to detect the newly discovered strains harboring a mecA variant. Such an amplification and detection reaction can be performed, e.g., in separate containers or in a single container as a multiplex reaction. Thus, in addition to the reaction detecting a mecA variant, an assay can include a reaction to detect, e.g., a junction region of a standard (i.e., as described for SCCmec types I-X) SCCmec cassette insertion, a standard (i.e., as described for SCCmec types I-X) mecA gene, and/or an S. aureus-specific chromosomal region.

By “amplifying a portion of mecA DNA” is meant performing an amplification reaction on a sample that produces an amplification product that includes sequences corresponding to any portion of a mecA gene, for example, the region between primers comprising a nucleic acid sequence set forth in SEQ ID NOs:12 and 13. For example, a primer can comprise a nucleic acid sequence as set forth in SEQ ID NOs:12 and 13. Primers comprising these sequences and primers consisting essentially of these sequences can be utilized as well as primers consisting of these sequences. Amplification can be detected, for example, utilizing a probe comprising a nucleic acid sequence between the target nucleic acids of the primers, or using an intercalating dye. Primers and probes can be readily designed for hybridization to the known mecA sequence.

Junction. The present inventive method, in addition to amplifying the mecA variant, if present, can further comprise amplifying a methicillin-resistant Staphylococcus aureus (MRSA) which comprises an insertion of an SCCmec cassette within Staphylococcus aureus chromosomal DNA, wherein the SCCmec cassette comprises a mecA, by utilizing in an amplification reaction a second oligonucleotide set for amplification of a right extremity junction of SCCmec cassette with Staphylococcus aureus chromosomal DNA, the second oligonucleotide set comprising:

a. a first junction oligonucleotide having a nucleic acid sequence capable of specifically hybridizing within a region of chromosomal Staphylococcus aureus DNA in a right extremity junction region; and

b. a second junction oligonucleotide having a nucleic acid sequence capable of specifically hybridizing within a region of a right extremity junction region of the SCCmec cassette of the MRSA comprising a mecA,

wherein each of the first junction oligonucleotide and the second junction oligonucleotide is oriented such that, under amplification conditions, if the sample contains the MRSA comprising a mecA, the right junction is amplified. The second oligonucleotide set can further comprise a third junction oligonucleotide having a nucleic acid sequence capable of specifically hybridizing within a region of the MRSA between the hybridizing region of the first junction oligonucleotide and the hybridizing region of the second junction oligonucleotide, wherein if the sample contains the MRSA comprising the right extremity junction, hybridization of the third junction oligonucleotide is detected.

The third junction oligonucleotide can be a probe. The third junction oligonucleotide can have a nucleic acid sequence capable of specifically hybridizing within a region of a right extremity junction region of the SCCmec cassette, or it can have a nucleic acid sequence capable of specifically hybridizing within orfX. Alternatively, a method of detection such as use of an intercalating dye can be performed. The first junction oligonucleotide, which can function as an amplification primer, can have a nucleic acid sequence capable of specifically hybridizing within orfX.

Primers and probes used in any reaction of this invention are capable of specifically hybridizing with a target nucleic acid. Specific hybridization is known in the art, and, typically, specific hybridization is achieved through nucleic acid identity or high similarity of the primer/probe with the target nucleic acid and/or through use of stringent hybridization conditions (e.g., stringent temperature and/or salt conditions). Specific hybridization provides selective hybridization to the target within the reaction.

Typically, for amplification reactions other than that to amplify orfX-mecA variant nucleic acids (such as to amplify a junction, a non-variant mecA and/or an S. aureus chromosomal region), the primer is selected such that amplification product synthesized utilizing it and a second primer (located in an S. aureus genomic sequence) will be of approximately 100 to 350 nt in length. While PCR amplification can be designed to generate longer or shorter amplicons (e.g., 50, 100, 150, 200, 250, 300, 350, 400, 500, 600, 700, 800, 900, 1000 nt or longer), preferred amplicon lengths for either transcription-based (e.g., NASBA or TMA) or PCR-type reactions for detection of mecA, junction or chromosomal S. aureus genes in the present invention will be within about 100 to 300 nt (e.g., 150, 200, 250, 300 nt) in length. Additionally, for a multiplex amplification reaction, whether transcription-based or PCR-based, an amplicon in the range of 100 to 300 nt or shorter is preferable for these targets, to enhance sensitivity of the test. It is noted that the amplification utilizing a first oligonucleotide having a nucleic acid sequence capable of specifically hybridizing to a region of chromosomal Staphylococcus aureus DNA in an extremity junction region and a second oligonucleotide having a nucleic acid sequence capable of specifically hybridizing to a region of a mecA variant will have a longer amplicon than that typically used in other amplifications that can form part of the present assay. It is also noted that, as amplification methods are further developed and refined, longer amplicons may become possible and eventually routine and are encompassed by the present invention.

A primer oriented such that, “under amplification conditions, the junction is amplified” includes a primer oriented such that, upon hybridization to its specific target nucleic acid, and upon initiation of an amplification reaction including the primer, an amplicon is formed that includes the junction. Such a reaction is designed to amplify across the junction (i.e., to be in sufficiently close proximity of the junction so that a typical amplification reaction would extend across the junction). Thus a primer pair useful for amplifying a junction will typically hybridize to two regions that surround the junction and each primer will be oriented to hybridize in a 5′-3′ direction toward the junction. Typically, the primer would be designed to hybridize within 600 nt, 500 nt, 400 nt, 350 nt, 300 nt, 250 nt, 200 nt 150 nt, 100 nt, 50 nt, 30 nt, 25 nt, 20 nt, etc. of the junction. A probe for detecting an amplification product is therefore selected to be capable of specifically hybridizing within a region of a right extremity junction region of the SCCmec cassette between the target sequences of the primers. For example, the probe can hybridize within S. aureus genomic sequences (e.g., orfX, between the target sequence of the S. aureus probe and the junction) or within SCCmec (between the target sequence of the SCCmec primer and the junction) or across the junction. In certain embodiments, such a probe can specifically hybridize fully within or primarily within SCCmec cassette. In one embodiment, in which the probe specifically hybridizes primarily within SCCmec cassette, the region to which the probe hybridizes can additionally include the junction and, therefore, at least one, or two or three or a few nucleotides of orfX that abut the junction. Typically, the primer is selected such that amplification product synthesized utilizing it and a second primer (located in an S. aureus genomic sequence) will be of approximately 100 to 350 nt in length. While PCR amplification can be designed to generate longer amplicons (e.g., 150, 200, 250, 300, 350, 400, 500, 600, 700, 800, 900, 1000 nt or longer), preferred amplicon lengths for either transcription-based (e.g., NASBA or TMA) or PCR-type reactions for detection of mecA, junction or chromosomal S. aureus genes in the present invention will be within about 100 to 300 nt (e.g., 150, 200, 250, 300 nt) in length. Additionally, for a multiplex amplification reaction, whether transcription-based or PCR-based, an amplicon in the range of 100 to 300 nt or shorter is preferable for these targets, to enhance sensitivity of the test. Specific primers useful for amplifying extremity junction regions can readily be designed, given the teachings herein and knowledge and skill in the art.

As used in the claims, “amplification conditions” are those appropriate for a selected amplification reaction, as are known to those of skill in the art, such as are utilized in various amplification reactions. Such conditions can be optimized for a specific reaction, primers, etc. as also known by the skilled artisan. As is known, such amplification conditions include contact with the required reagents for the amplification, e.g., nucleotides and enzymes, as well as the appropriate selected temperature, salt and pH conditions, among other aspects. Furthermore, as used in the claims, a primer or probe may be a primer or probe set, i.e., multiple primers or probes. Such primer/probe sets can be utilized in a reaction in which more than one type or subtype of MRSA is desired to be amplified and/or detected, and wherein the nucleic acid sequence of the target MRSA region selected for hybridization of the primer and/or probe varies among types and/or subtypes. Individual primers/probes can be designed for each type or subtype, as exemplified herein.

mecA. The present method can additionally comprise amplifying a Staphylococcus aureus comprising mecA by utilizing in an amplification reaction a third oligonucleotide set for amplification of a mecA element comprising:

a. a first mecA oligonucleotide having a nucleic acid sequence capable of specifically hybridizing within a region of mecA; and

b. a second mecA oligonucleotide having a nucleic acid sequence capable of specifically hybridizing within a second region within mecA, wherein each of the first mecA oligonucleotide and the second mecA oligonucleotide is oriented such that, under amplification conditions, a portion of the mecA is amplified. The third oligonucleotide set can further comprise a third mecA oligonucleotide having a nucleic acid sequence capable of specifically hybridizing within a region of the mecA between the hybridizing region of the first mecA oligonucleotide and the hybridizing region of the second mecA oligonucleotide wherein if the sample contains the MRSA comprising mecA, hybridization of the third mecA oligonucleotide is detected. Alternatively, a method of detection such as use of an intercalating dye can be used. Examples of primers for mecA can include SEQ ID NOs:12 and 13.

By amplifying a portion of mecA DNA is meant performing an amplification reaction on a sample that produces an amplification product that includes sequences corresponding to any identifying portion of a mecA gene, for example, the region between primers comprising a nucleic acid sequence set forth in SEQ ID NOs:12 and 13. Amplification can be detected using a probe that hybridizes between the target nucleic acids of the primers or using an intercalating dye. Primers and probes can be readily designed for hybridization to the known mecA sequence.

S. aureus Chromosome. The present method can further comprise utilizing a fourth oligonucleotide set for amplification of a Staphylococcus aureus-specific chromosomal DNA comprising:

a. a first S. aureus oligonucleotide having a nucleic acid sequence capable of specifically hybridizing within a region within Staphylococcus aureus-specific chromosomal DNA; and

b. a second S. aureus oligonucleotide having a nucleic acid sequence capable of specifically hybridizing within a second region within Staphylococcus aureus-specific chromosomal DNA, wherein each of the first S. aureus oligonucleotide and the second S. aureus oligonucleotide is oriented such that, under amplification conditions, a portion of the S. aureus-specific DNA is amplified. The fourth oligonucleotide set can further comprise a third S. aureus oligonucleotide having a nucleic acid sequence capable of specifically hybridizing within a region of the S. aureus DNA between the hybridizing region of the first S. aureus oligonucleotide and the hybridizing region of the second S. aureus oligonucleotide, wherein if the sample contains the region of the S. aureus DNA between the hybridizing region of the first S. aureus oligonucleotide and the hybridizing region of the second S. aureus oligonucleotide, hybridization of the third oligonucleotide is detected. Such third S. aureus oligonucleotide can function as a probe. The Staphylococcus aureus-specific chromosomal DNA can be any known S. aureus-specific genomic region, such as within the genes spa, orfX or nuc. Examples of primers for spa can include SEQ ID NOs:24 and 25, and probe, SEQ ID NO:26. Examples of primers for orfX can include SEQ ID NOs:9 and 10, and probe, SEQ ID NO:11. Examples of primers for nuc can include SEQ ID NOs:27, 28 and 30, and probe, SEQ ID NO:29. Alternatively, a method of detection such as use of an intercalating dye can be performed.

The present invention comprises a method of amplifying in a sample a methicillin-resistant Staphylococcus aureus (MRSA) which comprises an insertion of an SCCmec cassette within Staphylococcus aureus chromosomal DNA, wherein the SCCmec cassette comprises mecA or a mecA variant element, the method comprising performing on the sample an amplification reaction utilizing

a. a first oligonucleotide set comprising:

-   -   1) a first mecA variant oligonucleotide having a nucleic acid         sequence capable of specifically hybridizing to a first region         of a mecA variant element, and     -   2) a second mecA variant oligonucleotide having a nucleic acid         sequence capable of specifically hybridizing to a second region         of a mecA variant element; and

b. a second oligonucleotide set comprising:

-   -   1) a first mecA oligonucleotide having a nucleic acid sequence         capable of specifically hybridizing to a first region of mecA,         and     -   2) a second mecA oligonucleotide having a nucleic acid sequence         capable of specifically hybridizing to a second region of mecA,         wherein each of the first oligonucleotide and the second         oligonucleotide is oriented such that, under amplification         conditions, if the sample contains the MRSA, the region of the         MRSA between the hybridizing region of the first oligonucleotide         and the hybridizing region of the second oligonucleotide is         amplified. The first oligonucleotide set can further comprise a         third mecA variant oligonucleotide capable of specifically         hybridizing within a region of the MRSA between the hybridizing         region of the first mecA variant oligonucleotide and the         hybridizing region of the second mecA variant oligonucleotide,         and wherein if the sample contains the MRSA comprising a mecA         variant element, hybridization of the third mecA variant         oligonucleotide is detected. The second oligonucleotide set can         further comprise a third mecA oligonucleotide capable of         specifically hybridizing within a region of the MRSA between the         hybridizing region of the first mecA oligonucleotide and the         hybridizing region of the second mecA oligonucleotide, and         wherein if the sample contains the MRSA comprising mecA,         hybridization of the third mecA oligonucleotide is detected.         Such third oligonucleotide can be a probe. Alternatively, a         method of detection such as use of an intercalating dye can be         performed. By way of example, the first mecA variant         oligonucleotide can comprise a nucleic acid sequence selected         from the group consisting of SEQ ID NOs:6, 7, 14, 15 and 20. The         second mecA variant oligonucleotide can comprise a nucleic acid         sequence selected from the group consisting of SEQ ID NOs:16, 17         and 21. The third mecA variant oligonucleotide can comprise a         nucleic acid sequence selected from the group consisting of SEQ         ID NOs:8, 18 and 19. In such a method, the mecA variant can be         mecA_(LGA251) or it can be another mecA variant.

Junction. The method of amplifying in a sample a methicillin-resistant Staphylococcus aureus (MRSA) which comprises an insertion of an SCCmec cassette within Staphylococcus aureus chromosomal DNA, wherein the SCCmec cassette comprises mecA or a mecA variant element, can further comprise amplification of additional MRSA and/or S. aureus elements. For example, the method can comprise amplifying a methicillin-resistant Staphylococcus aureus (MRSA) which comprises an insertion of an SCCmec cassette within Staphylococcus aureus chromosomal DNA, wherein the SCCmec cassette comprises a mecA, by utilizing in an amplification reaction a second oligonucleotide set for amplification of a right extremity junction of SCCmec cassette with Staphylococcus aureus chromosomal DNA, the second oligonucleotide set comprising:

a. a first junction oligonucleotide having a nucleic acid sequence capable of specifically hybridizing within a region of chromosomal Staphylococcus aureus DNA in a right extremity junction region; and

b. a second junction oligonucleotide having a nucleic acid sequence capable of specifically hybridizing within a region of a right extremity junction region of the SCCmec cassette of the MRSA comprising a mecA, Wherein each of the first junction oligonucleotide and the second junction oligonucleotide is oriented such that, under amplification conditions, if the sample contains the MRSA comprising a mecA, the right junction is amplified. The third oligonucleotide set can further comprise a third junction oligonucleotide having a nucleic acid sequence capable of specifically hybridizing within a region of the MRSA between the hybridizing region of the first junction oligonucleotide and the hybridizing region of the second junction oligonucleotide, wherein if the sample contains the MRSA comprising the right extremity junction, hybridization of the third junction oligonucleotide is detected. The third junction oligonucleotide can have a nucleic acid sequence capable of specifically hybridizing within a region of a right extremity junction region of the SCCmec cassette. The first junction oligonucleotide can have a nucleic acid sequence capable of specifically hybridizing within orfX. The third junction oligonucleotide can have a nucleic acid sequence capable of specifically hybridizing within orfX. Alternatively, a method of detection such as use of an intercalating dye can be performed.

S. aureus. The method of amplifying in a sample a methicillin-resistant Staphylococcus aureus (MRSA) which comprises an insertion of an SCCmec cassette within Staphylococcus aureus chromosomal DNA, wherein the SCCmec cassette comprises mecA or a mecA variant element, can further comprise utilizing a fourth oligonucleotide set for amplification of a Staphylococcus aureus-specific chromosomal DNA comprising:

a. a first S. aureus oligonucleotide having a nucleic acid sequence capable of specifically hybridizing within a region within Staphylococcus aureus-specific chromosomal DNA; and

b. a second S. aureus oligonucleotide having a nucleic acid sequence capable of specifically hybridizing within a second region within Staphylococcus aureus-specific chromosomal DNA, wherein each of the first S. aureus oligonucleotide and the second S. aureus oligonucleotide is oriented such that, under amplification conditions, a portion of the S. aureus-specific DNA is amplified. The fourth oligonucleotide set can further comprise a third S. aureus oligonucleotide having a nucleic acid sequence capable of specifically hybridizing within a region of the S. aureus DNA between the hybridizing region of the first S. aureus oligonucleotide and the hybridizing region of the second S. aureus oligonucleotide, wherein if the sample contains the region of the S. aureus DNA between the hybridizing region of the first S. aureus oligonucleotide and the hybridizing region of the second S. aureus oligonucleotide, hybridization of the third oligonucleotide is detected. Such third S. aureus oligonucleotide can function as a probe. Alternatively, a method of detection such as use of an intercalating dye can be performed. The Staphylococcus aureus-specific chromosomal DNA can be selected from, for example, spa, orfX and nuc; however, other S. aureus-specific chromosomal DNA targets, as may be known to those of skill in the art, may be used.

It is to be recognized that, in addition to the amplification reaction detecting the presence of mecA variant, the invention includes that one can additionally amplify one or more additional relevant sequences, such as the SCCmec junction for SCCmec types other than those bearing mecA variant, mecA (non-variant), and an S. aureus-specific chromosomal sequence. One can combine any or all of these additional amplification reactions, in a multiplex reaction or in individual reactions.

A multiplex amplification reaction means that the specific reagents for amplification of more than one target are contacted together, such that more than one amplification can occur within the same reaction container. Additionally, detection reagents for more than one target can be included. Thus one can conduct a multiplex amplification and detection reaction by placing into contact all of the specific reagents for amplification and detection of more than one target.

Thus, in a multiplex reaction, one can amplify multiple target regions in the same reaction. Multiple amplification reactions can also be run sequentially. Simultaneous amplification can also be utilized, if a multiplex is not desired or feasible, wherein individual reactions are allowed to proceed at the same time, but the reagents for more than one amplification reaction are not necessarily all within the same reaction container or tube, but rather are carried out in separate reaction containers. It is understood that, even in a multiplex amplification reaction, each reaction will occur at whatever pace the individual reactions proceed under the provided conditions.

Detection can also be “simultaneous,” meaning that, if appropriate probes for each reaction in the reaction container are included, under the appropriate conditions, detection of more than one target can be achieved in either a single reaction container (multiplex) or in more than one reaction container (appropriate probes distributed to the relevant reaction container). Such detection can be performed, if desired, in the same reaction container as the multiplex or simultaneous amplification reaction, and, further, can be performed while amplification reactions continue (i.e., real-time). In the single container can be included all components of a reaction mixture, tailored to the specific amplification and detection method utilized. Thus, a “reaction mixture” can include all the necessary reagents for performing a reaction, which may include, but not be limited to, buffering agents to maintain pH at a selected level during a reaction, salts, co-factors, scavengers, and the like.

As used in the claims, “amplification conditions” are those appropriate for a selected amplification reaction, as are known to those of skill in the art, such as are utilized in various amplification reactions. Such conditions can be optimized for a specific reaction, primers, etc. as also known by the skilled artisan. As is known, such amplification conditions include contact with the required reagents for the amplification, e.g., nucleotides and enzymes, as well as the appropriate selected temperature, salt and pH conditions, among other aspects. Furthermore, as used in the claims, a primer or probe may be a primer or probe set, i.e., multiple primers or probes. Such primer/probe sets can be utilized in a reaction in which more than one type or subtype of MRSA is desired to be amplified and/or detected, and wherein the nucleic acid sequence of the target MRSA region selected for hybridization of the primer and/or probe varies among types and/or subtypes. Individual primers/probes can be designed for each type or subtype, as exemplified herein.

As used herein, an oligonucleotide “having” a nucleic acid sequence included in a portion of target DNA means the sequence has sufficient identity to the target DNA sequence, or its complement, to specifically and selectively hybridize to that target DNA under stringent hybridization conditions. It includes nucleic acid sequences having full sequence identity to the sequence.

Generally, amplification reactions producing amplicons (the product of a polynucleotide amplification reaction) are “template-driven” in that base pairing of reagents, either nucleotides or oligonucleotides, have complements in a template polynucleotide that are required for the creation of reaction products. In one aspect, template-driven reactions are primer extensions with a nucleic acid polymerase or oligonucleotide ligations with a nucleic acid ligase. Amplification can include any known or newly designed method of amplification, including those used in published methods (e.g., transcription-based amplification such as transcription-mediated amplification (TMA) and nucleic acid sequence-based amplification NASBA (as exemplified herein), and cycling nucleic acid amplification technologies (thermocycling) such as polymerase chain reaction (PCR), reverse transcriptase PCR (RT-PCR), and ligase chain reaction (LCR), and any method of amplification, e.g., sustained sequence replication (3SR), strand displacement amplification (SDA), branched DNA (bDNA), cycling probe technology (CPT), solid phase amplification (SPA), rolling circle amplification technology (RCA), solid phase RCA, anchored SDA and nuclease dependent signal amplification (NDSA), all of which are known to the skilled artisan. An amplification reaction may be a “real-time” amplification if a detection chemistry is available that permits a reaction product to be measured as the amplification reaction progresses, e.g. real-time PCR or real-time NASBA. Thus this invention includes the use of any nucleic acid amplification method or any other procedure which may be used to increase the sensitivity and/or the rapidity of nucleic acid-based diagnostic tests. The present invention also includes the use of any detection technology including post-amplification detection technologies, any amplification technology combined with detection, any hybridization nucleic acid chips or array technologies, and any amplification chips or combination of amplification and hybridization chip technologies. Detection and identification by any nucleotide sequencing method is also within the present invention.

A variety of detection methods can be utilized in this invention, Detection methods utilizing nucleic acid probes are well known in the art. Probes of the present kits and/or for use in the present methods can be labeled by any selected label suitable for the detection method chosen, many of which are known in the art, such as a phosphatase (e.g., alkaline phosphatase), biotin, avidin, a peroxidase (e.g., horseradish peroxidase), digoxigenin, a fluorescent dye (such as Cy3 and Cy5 dyes, fluorescein, FAM, ROX), a chemiluminescent label, a chromophoric label, a radioactive label (e.g., a radioisotope) and a ligand. Probe designs for different detection methods can be used, such as target-capture, HPA, TaqMan, molecular beacons, scorpions and sandwich hybridization. Hybridization conditions can be selected in accordance with the type of probe and the type of detection reaction selected. Additionally, intercalating dyes can be utilized. An intercalating dye is one that binds specifically to double-stranded DNA fluoresce brightly upon such binding; in the absence of double stranded DNA, with nothing to bind to they only fluoresce at a low level. Detection is monitored by measuring the increase in fluorescence throughout the amplification cycle. An intercalating dye can, if desired, be used with melt analysis, as is known in the art. Examples of intercalating dyes can include, but are not limited to, ethidium bromide, SYBR® Green, LC Green, LC Green Plus, ResoLight, EvaGreen, Chromofy and SYTO 9. Others will be known to those of skill in the art and new such dyes may become available.

The present method further provides useful kits for use in such amplification and detection methods, Specifically, the present invention provides a kit for amplifying a methicillin-resistant Staphylococcus aureus (MRSA) which comprises an insertion of an SCCmec cassette within Staphylococcus aureus chromosomal DNA, wherein the SCCmec cassette comprises a mecA variant element, the kit comprising a first oligonucleotide set comprising:

a. a first oligonucleotide having a nucleic acid sequence capable of specifically hybridizing to a region of chromosomal Staphylococcus aureus DNA in an extremity junction region, and

b. a second oligonucleotide having a nucleic acid sequence capable of specifically hybridizing to a region of a mecA variant. Such kit can further comprise a third oligonucleotide capable of specifically hybridizing within a region of the MRSA between the hybridizing region of the first oligonucleotide and the hybridizing region of the second oligonucleotide. Such third oligonucotide can be a probe. In a preferred embodiment, the first oligonucleotide comprises a nucleic acid sequence selected from the group consisting of SEQ ID NOs:9 and 10. Also in a preferred embodiment, the second oligonucleotide comprises a nucleic acid sequence selected from the group consisting of: SEQ ID NOs:6, 7, 14, 15, 16, 17, 20 and 21. Further, in another preferred embodiment, the third oligonucleotide comprises a nucleic acid sequence set forth as SEQ ID NOs:8, 11, 18 and 19. The mecA variant for which this kit is useful to detect can be mecA_(LGA251) or another mecA variant.

A kit of the present invention, for amplifying a methicillin-resistant Staphylococcus aureus (MRSA) which comprises an insertion of an SCCmec cassette within Staphylococcus aureus chromosomal DNA, wherein the SCCmec cassette comprises a mecA variant element, can further comprise one or more additional elements, including oligonucleotide sets for detection of additional MRSA and MSSA elements. Though sometimes described herein as “second,” “third” or “fourth” oligonucleotide sets, choice of an additional nucleotide set is independent of the other options. For example, the kit can include oligonucleotide sets for amplification of one or more of the SCCmec junction for SCCmec types other than those bearing mecA variant, mecA (non-variant), and a S. aureus chromosomal sequence. In one example, a kit can comprise a second oligonucleotide set comprising:

a. a first junction oligonucleotide having a nucleic acid sequence capable of specifically hybridizing within a region of chromosomal Staphylococcus aureus DNA in a right extremity junction region; and

b. a second junction oligonucleotide having a nucleic acid sequence capable of specifically hybridizing within a region of a right extremity junction region of the SCCmec cassette. In another example, the kit can comprise a third oligonucleotide set for amplification of a mecA element comprising:

a. a first mecA oligonucleotide having a nucleic acid sequence capable of specifically hybridizing within a region of mecA DNA; and

b. a second mecA oligonucleotide having a nucleic acid sequence capable of specifically hybridizing within a second region within mecA DNA. Another example provides that the kit can comprise a fourth oligonucleotide set for amplification of a Staphylococcus aureus-specific chromosomal DNA comprising:

a. a first S. aureus oligonucleotide having a nucleic acid sequence capable of specifically hybridizing within a region within Staphylococcus aureus-specific chromosomal DNA; and

b. a second S. aureus oligonucleotide having a nucleic acid sequence capable of specifically hybridizing within a second region within Staphylococcus aureus-specific chromosomal DNA.

Another kit of the present invention provides a kit for amplifying in a sample a methicillin-resistant Staphylococcus aureus (MRSA) which comprises an insertion of an SCCmec cassette within Staphylococcus aureus chromosomal DNA, wherein the SCCmec cassette comprises mecA or a mecA variant element, wherein the SCCmec cassette comprises mecA or a mecA variant element.

a) a first oligonucleotide set comprising:

-   -   1) a first mecA variant oligonucleotide having a nucleic acid         sequence capable of specifically hybridizing to a first region         of a mecA variant element, and     -   2) a second mecA variant oligonucleotide having a nucleic acid         sequence capable of specifically hybridizing to a second region         of a mecA variant element; and

b) a second oligonucleotide set comprising:

-   -   1) a first mecA oligonucleotide having a nucleic acid sequence         capable of specifically hybridizing to a first region of mecA,         and     -   2) a second mecA oligonucleotide having a nucleic acid sequence         capable of specifically hybridizing to a second region of mecA.         The kit can further comprise in the first oligonucleotide set a         third mecA variant oligonucleotide capable of specifically         hybridizing within a region of the MRSA between the hybridizing         region of the first oligonucleotide and the hybridizing region         of the second oligonucleotide. It can comprise in the second         oligonucleotide set a third mecA oligonucleotide capable of         specifically hybridizing within a region of the MRSA between the         hybridizing region of the first oligonucleotide and the         hybridizing region of the second oligonucleotide. In a specific         example, the first mecA variant oligonucleotide can comprise a         nucleic acid sequence selected from the group consisting of SEQ         ID NOs:9 and 10. In another example, the second mecA variant         oligonucleotide comprises a nucleic acid sequence selected from         the group consisting of SEQ ID NOs:6, 7, 14, 15, 16, 17, 20         and 21. In another embodiment, in the first oligonucleotide set,         the third mecA variant oligonucleotide comprises a nucleic acid         sequence set forth as SEQ ID NOs:8, 18 and 19. In any such kit,         the mecA variant can preferably be mecA_(LGA251); however, it         can be another mecA variant.

A kit of this invention can further comprise a third oligonucleotide set comprising: a. a first junction oligonucleotide having a nucleic acid sequence capable of specifically hybridizing within a region of chromosomal Staphylococcus aureus DNA in a right extremity junction region; and b. a second junction oligonucleotide having a nucleic acid sequence capable of specifically hybridizing within a region of a right extremity junction region of the SCCmec cassette comprising mecA, wherein each of the first junction oligonucleotide and the second junction oligonucleotide is oriented such that, under amplification conditions in the presence of the MRSA wherein the SCCmec cassette comprises mecA, an SCCmec cassette right insertion junction is amplified. The third oligonucleotide set can further comprise a third junction oligonucleotide having a nucleic acid sequence capable of specifically hybridizing within a region of the MRSA between the hybridizing region of the first junction oligonucleotide and the hybridizing region of the second junction oligonucleotide.

A kit of this invention can further comprise a fourth oligonucleotide set comprising:

a. a first S. aureus oligonucleotide having a nucleic acid sequence capable of specifically hybridizing within a region within Staphylococcus aureus-specific chromosomal DNA; and

b. a second S. aureus oligonucleotide having a nucleic acid sequence capable of specifically hybridizing within a second region within Staphylococcus aureus-specific chromosomal DNA, wherein each of the first S. aureus oligonucleotide and the second S. aureus oligonucleotide is oriented such that, under amplification conditions in the presence of an MRSA, a portion of S. aureus-specific DNA is amplified. The fourth oligonucleotide set can further comprise a third S. aureus oligonucleotide having a nucleic acid sequence capable of specifically hybridizing within a region of the S. aureus DNA between the hybridizing region of the first S. aureus oligonucleotide and the hybridizing region of the second S. aureus oligonucleotide

Probes of this invention, including those included in such kits, can advantageously be labeled for detection, as known by persons of skill in the art. Labels can appropriately be selected for the specific design and type of amplification reaction to be performed. Primer and probe reagents can be provided in any of several states, including dried, lyophilized, pelleted, spray-dried, or in liquid.

Kits of this invention can include additional elements, such as reagents for a selected amplification method (e.g., amplification enzyme(s), buffer(s), and/or restriction enzyme(s), among others), control(s), reaction container(s), and the like. If an intercalating dye is to be used, such can be included in the kit. Additionally, a kit of the present invention can comprise a container comprising a kit as described herein. Elements can be provided in a single container or in more than one container. Such kits can be useful for performing multiplex amplifications.

It is noted that references to primer and probe sequences that include thymidine can be readily adapted to utilize uridine in substitution for thymidine, where useful for the particular assay. Furthermore, nucleotides may be modified by addition of chemical groups, or substitution of individual residues by analogues (e.g., 2′-O-methoxy versions). Additional such modified nucleotides are known in the art; some examples include hydroxymethyl nucleotides, methylated nucleotides, fluorinated nucleotides, alpha thio phosphate nucleotides, amine-modified nucleotides, methoxy nucleotides, carboxymethyl nucleotides, thio nucleotides, inosine, dihydrouridine, pseudouridine, wybutosine, queuosine, C7dGTP. Additional modified nucleotides are found in U.S. Pat. Nos. 5,405,950 and 5,633,364 (both, Mock and Lovern). Furthermore, a probe can comprise DNA, RNA, modified DNA or RNA, PNA, other synthetic nucleic acids or nucleic acid substitutes that use nucleotide bases as means of selectively hybridizing to a target.

The present method can be utilized on any selected sample, such as a direct patient sample, e.g., nasal or inguinal swab, perineum swab, axilla swab, throat swab, rectal swab, samples from wounds, all particularly suitable for screening, as well as particularly suitable for diagnosis, bronchoalveolar lavage or blood (e.g., septicemia or blood culture). Such samples typically contain a mixed population of organisms. Additionally, if desired, this method can be applied to a sample having only a single bacterial species or strain, e.g., samples utilizing isolation, culture, capture, and/or enrichment of MRSA.

The present invention is exemplified in the following examples. As taught throughout the specification, detection of mecA variant can be combined in any desired combination, in multiplex or multiple simplex form, with another desired assay, such as primers and/or probe(s) for mecA, genomic S. aureus and/or SCCmec junction.

EXAMPLES Amplification Conditions

Amplifications using PCR can be performed under standard conditions. Such conditions can include:

MIX Preparation (Reaction Performed in 25 μL):

Initial Final concentra- Concentra- for 1 sample Reagent tion tion (volume in μL) Water NA NA 16.15 Buffer pH 8.6 50X 1X 0.50 (KCL 50 mM) MgCl2 solution 1M 5.4 mM 0.14 Dntp 10 mM 0.124 mM 0.31 KCl 1.2M   14.8 mM 0.31 Forward Primer 20 μM 0.2 μM 0.25 Reverse Primer 20 μM 0.2 μM 0.25 Probe 20 μM 0.1 μM 0.13 BSA 10 μg/μL 0.5 μg/μL 1.25 Fast Start enzyme 5 U/μL 0.112 U/μL (3.6 U/rxn) 0.72 Target (μl) NA NA 5 Amplification Cycle on Biorad CFX96

Annealing/ Enzyme Extending activation Denaturation (optic on) Temperature (° C.) 95 95 65 Time (sec) 300 5 30 Cycle(s) 1 50 Oligonucleotide Design

Oligonucleotides dedicated to amplification or detection and belonging to genomic regions described herein can be utilized whatever the method used for their design. Among these methods which can be used are, for example (without being limited), design by hand (human expertise in oligonucleotide design) or design using computer means (scripts, programs, software) Eberhardt N L, A shell program for the design of PCR primers using genetics computer group (GCG) software (7.1) on VAX/VMS systems, Biotechniques 1992 December; 13(6):914-7); Mitsuhashi M., Technical report: Part 1. Basic requirements for designing optimal oligonucleotide probe sequences. J Clin Lab Anal 1996; 10(5):277-84).

Example 1 Design of mecA Variant Primers and Probes

Experiments were designed to develop a PCR amplifying the Staphylococcus aureus orfX-mecA variant region. Initially, to design primer(s) on the orfX side of the SCCmec junction, two primers and one probe were designed in the orfX region. A mecA variant-specific set of oligos (for mecA_(LGA251), also described in literature as mecA_(M10/0061), mecA homologue, and mecA_(new variant)) were also designed. As the mecA variant orientation was initially unknown, we designed mecA variant divergent primers in order to obtain a mecA variant-orfX amplicon. Further candidates on both ends of mecA variant gene have been designed to develop specific PCR of Staphylococcus aureus. The PCR assay selected for mecA variant amplification across the SCCmec junction should generate an amplicon about 1300 nt long. The PCR assay selected for detection of the mecA variant element itself may vary from this amplicon size; for example, it may produce a shorter amplicon.

A mecA variant reference sequence was found on NCBI with the following accession number; FR823292 and utilized for initial primer design. A first step was to design mecA variant-specific oligos. As the mecA variant orientation was initially unknown, mecA variant divergent primers (both at 5′ and 3′ ends of the mecA variant gene) were designed in order to obtain a mecA variant-orfX amplicon.

Design on 5′ End of mecA Variant Gene

Standard PCR conditions, as described above, were utilized, unless noted differently.

Primer Design

Many primers were designed (data not shown); two were selected based on thermodynamic characteristics:

TABLE 1 5′_forward primers characteristics mecAv-orfX-1 mecAv-orfX-2 (SEQ ID NO: 1) (SEQ ID NO: 2) FR823292, 5′ 3613 3614 end position Sequence ATGAAGCAATATCAAAGGA TGAAGCAATATCAAAGGAA (5′->3′) Oligo length 19 nt 19 nt Tm 59° C. 60° C. % GC 31% 31% Hairpin NO- NO- formation Intra-molecular Intra-molecular risk structure stable structure stable assessment (Intramolec- ular Folding workflow) Primer Dimer NO Primer-dimer NO Primer-dimer risk risk predicted risk predicted assessment (Hybridiza- tion workflow)

Probe Design

Many probes for the 5′ end of mecA variant were designed (data not shown), and three were selected based on thermodynamic characteristics:

TABLE 2 5′ probes characteristics mecAv-orfX-3 mecAv-orfX-4 mecAv-orfX-5 (SEQ ID NO: 3) (SEQ ID NO: 4) (SEQ ID NO: 5) FR823292, 5′ end 3657 3655 3653 position Sequence (5′->3′) ATAACTTGGTTATTCA ACTTGGTTATTCAAAG TGGTTATTCAAAGATG AAGATGACGATATT ATGACGATATTGA ACGATATTGAGA Oligo length 30 nt 29 nt 28 nt Tm (Apollo PCR 69° C. 68° C. 67° C. default) % GC 26% 31% 32% Hairpin formation NO- NO- NO- risk assessment Intra-molecular Intra-molecular Intra-molecular (intramolecular structure stable structure stable structure stable Folding workflow) Primer Dimer risk NO Primer-dimer NO Primer-dimer NO Primer-dimer assessment risk predicted risk predicted risk predicted (Hybridization workflow) Design on 3′ End of mecA Variant Gene

Primer Design

Many forward primers for 3′end of mecA variant gene were designed (data not shown), and two of them were selected based on thermodynamic characteristics:

TABLE 3 mecA variant 3′forward primers characteristics mecAv-orfX-6 mecAv-orfX-7 (SEQ ID NO: 6) (SEQ ID NO: 7) FR823292, 5′ end position 1877 1863 Sequence (5′->3′) ATCCTAATATGTTAATGGCGA ATGGCGATTAATGTTAAAGA Oligo length 21 nt 20 nt Tm (Apollo PCR default) 62° C. 61° C. % GC 33% 30% Hairpin formation risk NO- NO- assessment (Intramolecular Intra-molecular Intra-molecular Folding workflow) structure stable structure stable Primer Dimer risk NO Primer-dimer NO Primer-dimer assessment risk predicted risk predicted (Hybridization workflow)

Probe Design

Many probes for 3′end of mecA variant gene were designed (see Table 4; additional data not shown), and one was selected based on thermodynamic characteristics:

TABLE 4 mecA variant 3′probe characteristics mecAv-orfX-8 (SEQ ID NO: 8) FR823292, 1826 5′ end position Sequence (5′-3′) TGGCCAGCTATAATGCTACTATATCTGGA Oligo length 29 nt Tm (Apollo PCR 71° C. default) % GC 41% Hairpin formation NO- risk assessment Intra-molecular structure (Intramolecular stable Folding workflow) Primer Dimer risk NO Primer-dimer risk predicted assessment (Hybridization workflow) Oligos Compatibility

Input parameters: Temperature: 63° C.; [Na+]: 0.05 M; [Mg2+]: 0.005 M; Strand concentration: 0.00001 M

TABLE 5 mecA variant oligonucleotide compatibility; Free Energy Unit is Kcal/mol MecA variant MecA variant MecA variant MecA variant MecA variant MecA variant MecA variant MecA variant Primer mecAv- Primer mecAv- Probe mecAv- Probe mecAv- Probe mecAv- Primer mecAv- Primer mecAv- Probe mecAv- orfX-1 orfX-2 orfX-3 orfX-4 orfX-5 orfX-6 orfX-7 orfX-8 (SEQ ID (SEQ ID (SEQ ID (SEQ ID (SEQ ID (SEQ ID (SEQ ID (SEQ ID DG NO: 1) NO: 2) NO: 3) NO: 4) NO: 5) NO: 6) NO: 7) NO: 8) MecA variant −1.09 −1.56 −1.56 −1.56 −1.56 −1.4 −1.4 −0.8 Primer mecAv-orfX-1 MecA variant −1.56 −1.09 −1.56 −1.56 −1.56 −1.6 −1.4 −0.64 Primer mecAv-orfX-2 MecA variant −1.56 −1.56 −1.09 −1.56 −1.56 −1.4 −1.4 −1.04 Probe mecAv-orfX-3 MecA variant −1.56 −1.56 −1.56 −1.09 −1.56 −1.4 −1.4 −1.04 Probe mecAv-orfX-4 MecA variant −1.56 −1.56 −1.56 −1.56 −1.09 −1.4 −1.4 −1.04 Probe mecAv-orfX-5 MecA variant −1.4 −1.6 −1.4 −1.4 −1.4 −0.77 −1.24 −1.77 Primer mecAv-orfX-6 MecA variant −1.4 −1.4 −1.4 −1.4 −1.4 −1.24 −0.77 −1.77 Primer mecAv-orfX-7 MecA variant −0.8 −0.64 −1.04 −1.04 −1.04 −1.77 −1.77 −2.88 Probe mecAv-orfX-8

All the above oligonucleotides were found to be compatible together and also compatible with oligonucleotides designed and selected in the orfX (see below). These experiments provided the orientation of mecA variant gene and conclude that oligos designed in 3′-end of mecA variant will be used for a mecA variant-orfX amplification reaction.

Example 2 mecA Variant-orfX Amplification Reaction

Standard PCR conditions, as described above, were utilized, unless noted differently.

Example 2a Selection of Primers

Tests were performed on one mecA variant (+) strain (Internal collection strain number 1156001) at 10 ng/μl, and one mecA(+) strains (ATCC 43300 strain) at 10 ng/μl. Primers tested were:

orfX MRSA primers:

-   -   mecAv-orfX-9 (SEQ ID NO:9): 10 μM     -   mecAv-orfX-10 (SEQ ID NO:10): 10 μM

mecA variant 3′-end primers:

-   -   mecAv-orfX-6 (SEQ ID NO:6): 10 μM     -   mecAv-orfX-7 (SEQ ID NO:7): 10 μM

Conditions for all PCR reactions for primer selection were as follows:

-   -   PCR format: 45 μl MIX+5 μl target     -   PCR conditions: 4 conditions have been tested (see below)     -   Expand High Fidelity PCR system (Roche, ref 11732650001, Lot         Number 11398326)     -   GeneAmp PCR system 9700

TABLE 6 PCR 4 tested conditions: Temperature Time Cycle Condition 1/thermo n°20555 95° C. 2 min 1 cycle 95° C. 30 s 55° C. 20 s 30 cycles 72° C. 30 s 72° C. 7 min 1 cycle  4° C. infinite 1 cycle Condition 2/thermo n°20556 94° C. 2 min 1 cycle 94° C. 15 s 55° C. 30 s 30 cycles 72° C. 45 s 72° C. 7 min 1 cycle  4° C. infinite 1 cycle Condition 3/thermo n°20557 95° C. 5 min 1 cycle 95° C. 30 s 55° C. 45 s 35 cycles 72° C. 1 min 72° C. 7 min 1 cycle  4° C. infinite 1 cycle Condition 4/thermo n°20596 95° C. 5 min 1 cycle 95° C. 1 min 55° C. 1′30 35 cycles 72° C. 2 min 72° C. 7 min 1 cycle  4° C. infinite 1 cycle

The following primers that selectively hybridize in mecA variant (mecA_(LGA251)) were tested in the listed specific conditions:

-   -   MIX 1: positive control for mecA variant     -   MIX 2: test oligo mecAv-orfX-6 (SEQ ID NO:6) in mecA variant         (amplicon 1498 nt long)     -   MIX 3: test oligo mecAv-orfX-7 (SEQ ID NO:7) in mecA variant         (amplicon 1484 nt long)

TABLE 7 Reagent MIX/tube Final Concentration] Positive Control MIX 1: Positive Control 4 tubes Buffer 10X 5 μl 1X 20 μl MgCl2 25 mM 3 μl 1.5 mM 12 μl dNTP 25 mM 0.4 μl 0.2 mM 1.6 μl Primer + Control 10 μM 2 μl 0.4 μM 8 μl Primer + Control 10 μM 2 μl 0.4 μM 8 μl Enzyme 3.5 U/μl 0.74 μl 2.6 U 3 μl H₂O acros qsp 45 μl 31.86 μl NA 127.4 μl Total MIX 45 μl 180 μl Target: DNA 10 ng/μl 5 μl 50 ng TOTAL 50 μl orfX- mecA variant Assay MIX 2: mecAv-orfX-9/mecAv-orfX-10/mecAv-orfX-6 10 tubes Buffer 10X 5 μl 1X 50 μl MgCl2 25 mM 8 μl 4 mM 80 μl dNTP 25 mM 1.2 μl 0.6 mM 12 μl mecAv-orfX-9 10 μM 3 μl 0.6 μM 30 μl mecAv-orfX-10 10 μM 3 μl 0.6 μM 30 μl mecAv-orfX-6 10 μM 3 μl 0.6 μM 30 μl Enzyme 3.5 U/μl 1 μl 3.5 U 10 μl H₂O acros qsp 45 μl 20.8 μl NA 208 μl* Total MIX 45 μl 450 μl Target: DNA 10 ng/μl 5 μl 50 ng TOTAL 50 μl orfX- mecA variant Assay MIX 3: mecAv-orfX-9/mecAv-orfX-10/mecAv-orfX-7 Buffer 10X 5 μl 1X 50 μl MgCl2 25 mM 8 μl 4 mM 80 μl dNTP 25 mM 1.2 μl 0.6 mM 12 μl mecAv-orfX-9 10 μM 3 μl 0.6 μM 30 μl mecAv-orfX-10 10 μM 3 μl 0.6 μM 30 μl mecAv-orfX-7 10 μM 3 μl 0.6 μM 30 μl Enzyme 3.5 U/μl 1 μl 3.5 U 10 μl H₂O acros qsp 45 μl 20.8 μl NA 208 μl* Total MIX 45 μl 450 μl Target: DNA 10 ng/μl 5 μl 50 ng TOTAL 50 μl Results/Conclusions of Assay:

TABLE 8 Results of orfX- mecA variant Assay: Results mecA variant condition condition condition condition Sample ID condition 1 1 2 3 4 orfX- mecA variant (mecAv-orfX-6) strain #1156001 + + + + + from internal strain collection ATCC 43300 − − − − NA strain H2O − − − − NA orfX- mecA variant (mecAv-orfX-7) strain #1156001 + + + + + from internal strain collection ATCC 43300 − − − − NA strain H₂O − − − − NA

All conditions are found to be working: positive results were obtained for mecA variant and negative results were obtained for mecA. Both mecA variant primers were effective in amplifying the mecA variant-orfX amplicon and therefore for use in an assay to detect mecA variant-bearing MRSA strains. Details of an orfX-mecA variant PCR using orfX primer mecAv-orfX-9, mecA variant primer mecAv-orfX-7 and orfX primer mecAv-orfX-10 that was prepared and conducted is provided below. Successful amplification of the mecA variant (mecA_(LGA251)) was achieved.

TABLE 9 OrfX-mecA variant PCR: MIX: PCR orfX-mecA variant Reagent Initial [C] Final Concentration Vol/tube Buffer 10X 1X 5 μl MgCl₂ 25 mM 4 mM 8 μl dNTP 25 mM 0.6 mM 1.2 μl mecAv-orfX-9 10 μM 0.6 μM 3 μl mecAv-orfX-10 10 μM 0.6 μM 3 μl mecAv-orfX-7 10 μM 0.6 μM 3 μl Enzyme 3.5 U/μl 3.5 U 1 μl H₂O acros qsp 45 μl NA NA 20.8 μl Total MIX 45 μl DNA 10 ng/μl 50 ng 5 μl TOTAL 50 μl Cycles PCR Temperature Time Cycle 94° C. 2 min 1 cycle 94° C. 15 s 55° C. 30 s 30 cycles 72° C. 45 s 72° C. 7 min 1 cycle  4° C. infinite 1 cycle

Example 2b Amplification with Probe in orfX and Probe in the mecA Variant Gene

Next, probe was added and the PCR was tested on Bio-Rad instrument (real time PCR system). Tests were done with TaqMan probe either in the orfX (mecAv-orfX-11 (SEQ ID NO:11)) or in the mecA variant gene (mecA_(LGA251): 3′ end) (mecAv-orfX-8 (SEQ ID NO:8)) (see below). The fluorophore used for both Taqman probes is FAM. DNA from five samples (10 ng/μl) was tested.

SEQ ID Probe NO Sequence (5′->3′) mecAv-orfX-11 11 TGATGCGGGTTGTGTTAATTGAGCAAGTG mecAv-orfX-8  8 TGGCCAGCTATAATGCTACTATATCTGGA

Amplifications were performed under the following conditions:

-   PCR format: 45 μl MIX+5 μl target -   PCR conditions: 2 probes were tested at 2 concentrations (0.3 μM and     0.6 μM) -   Expand High Fidelity PCR system (Roche, ref 11732650001, lot number     11398326) -   The following combinations of primers and probes (all, 10 μM) were     utilized. -   MIX 1: mecAv-orfX-9/mecAv-orfX-10/mecAv-orfX-7/mecAv-orfX-11 at     0.6±μM -   MIX 2: mecAv-orfX-9/mecAv-orfX-10/mecAv-orfX-7/mecAv-orfX-11 at 0.3     μM -   MIX 3: mecAv-orfX-9/mecAv-orfX-10/mecAv-orfX-7/mecAv-orfX-8 at 0.6     μM -   MIX 4: mecAv-orfX-9/mecAv-orfX-10/mecAv-orfX-7/mecAv-orfX-8 at 0.3     μM     Results were as follows:

Results MIX 1 MIX 2 MIX 3 MIX 4 mecAv-orfX- mecAv-orfX- mecAv-orfX- mecAv-orfX- Sample 11/0.6 μM 11/0.3 μM 8/0.6 μM 8/0.3 μM Id Strains Cq End RFU Cq End RFU Cq End RFU Cq End RFU 1 mecAv (+) 29.51 65.5 21.61 819 28.48 90.9 17.92 1331 2 mecAv (+) 25.89 70.3 N/A 32.5 25.8 57.7 N/A 1.41 3 mecAv (+) 29.53 47.7 N/A 38.1 20.37 91.3 26.56 124 4 mecA (+) N/A 9.58 28.65 47.5 N/A −8.87 N/A 3.63 5 MSSA N/A 6.52 30.32 53 N/A −1.35 N/A 0.746 H₂O NA 6.37 172 N/A 1.36 N/A 3.26 N/A 0.0398 RFU: threshold with 40

The results indicate that ideal probe concentration, under these conditions, can be around 0.3 μM. Results with probe in orfX or in mecA variant gene both gave good results. In general, under these conditions, the test seems to be more specific with probe in mecA variant gene; however, one can adjust the parameters, such as conducting the annealing step at 55° C., to optimize the assay. Further optimization can also be done, for example, one can increase the number of cycles, add a FAM read after the last step at 72° C., and/or increase the annealing temperature. This experiment shows that on MRSA strains, a specific real time PCR is feasible between the orfX and mecA variant gene despite very long amplicons generated (around 1484 bp).

Example 3 Amplification of SCCmec:orfX Junction Region of Non-typeXI and of mecA

An assay can be performed in combination with an assay for SCCmec typeXI to additionally detect the presence or absence of non-typeXI SCCmec-carrying MRSA strains (those that harbor mecA). An assay can also be performed in combination with an assay for other sequences, such as S. aureus genomic region(s) and/or mecA to additionally characterize the organism(s) present in a sample. These assays can be performed in multiplex or separately.

Example 3a Detection of Right Extremity Junction Region

For detection of the right extremity junction in SCCmec types other than type XI, one can utilize, either in a multiplex with an assay to detect typeXI or separately, primers located in the right part of the SCCmec cassette and in the orfX. This reaction can use probes located either in the right part of the cassette or in the orfX. MRSA and MSSA strains can be tested using a lysate as target corresponding to 10⁵ CFU per amplification reaction or as directed for a specific kit. For example, commercially available kits that can be utilized to detect this junction include:

NucliSens EasyQ ® MRSA BioMerieux (Marcy l'Etoile, France) BD GeneOhm ™ MRSA Assay Becton Dickinson (Franklin Lakes, NJ) BD GeneOhm ™ MRSA ACP Becton Dickinson Assay BD MAX MRSA assay Becton Dickinson PLEX-ID MRSA assay Abbott (Ibis Biosciences) (Abott Park, IL) Detect-Ready ™ MRSA Assay Molecular Detection Inc. (MDI) (Wayne, PA) LightCycler ® MRSA Roche (Pleasanton, CA) Advanced Test Xpert MRSA Cepheid (Sunnyvale, CA) Xpert MRSA/SA BC Cepheid Xpert MRSA/SA SSTI Cepheid Additionally, primers can be designed using Path-MRSA or Path-MRSA std (both, Genesig).

Example 3b Multiplex Amplification and Detection of mecA Gene and Cassette Insertion (junction) Region

As shown in this example, simultaneous amplification and detection of both the insertion cassette region and the mecA gene can be utilized to reduce detection of certain strains (false MRSA positive) for non-typeXI strains. As described and exemplified in Jay, et al. (US20090203013; WO2009085221, incorporated by reference) and available commercially (NucliSens EasyQ® MRSA (bioMerieux, Marcy l'Etoile, France)), this strategy can be used for a multiplex amplification for detection of both the mecA gene and the cassette junction region in the same tube. In one example, the assay uses 5 SCCmec cassette-specific forward primers in SCCmec right extremity junction region, 1 reverse primer in orfX, and 5 labeled SCCmec cassette-specific probes for the cassette junction region in combination with 1 forward primer, 1 reverse primer and 1 labeled probe for mecA. The results of such an assay show that, in the case of an MSSA possessing the insertion cassette region without the mecA gene, this portion of the assay can properly provide a “MRSA negative” result (SCCmec junction (+) plus mecA (−)).

Example 4 Amplification of MRSA Genomic Region (spa)

Standard PCR conditions, as described above, are utilized, unless noted differently.

The S. aureus spa gene is a gene encoding the protein A, which is a surface protein found specifically in the cell wall of Staphylococcus aureus bacteria. One part of spa gene, the polymorphic region X, is highly variable and is used for the spa typing permitting to differentiate several S. aureus. However more conservative areas are also present in spa gene and are used as specific markers to detect all the S. aureus strains. [Kuhn, JCM2007, “Double-locus sequence typing using clfB and spa, a fast and simple method for epidemiological typing of methicillin-resistant Staphylococcus aureus”].

After building a multiple sequence alignment (from a collection of sequences from proprietary and/or public databanks), the oligonucleotides were designed in the conservative area of the gene. The resulting amplification and/or detection of the spa region demonstrate that S. aureus is present in the sample.

Oligonucleotides are as follows:

SEQ ID Oligo NO Sequence S.aureus-1 24 CACCTGCTGCAAATGCTG (18 nt) Primer S.aureus-2 25 CGTTGATCAGCRTTTAAGTTAGGCATATT  Primer (29 nt) S.aureus-3 26 CGCAACACGATGAAGCTCAACAAAATGC  Probe (28 nt)

Example 5 Amplification of MRSA Genomic Region (nuc)

The nuc gene encodes the S. aureus thermostable nuclease also called thermonuclease. This gene is S. aureus specific and is highly conserved [Bragstad et al. JCM 1992, “Detection of Staphylococcus aureus by polymerase chain reaction amplification of the nuc gene”].

After building a multiple sequence alignment (from a collection of sequences from proprietary and/or public databanks), the oligonucleotides were designed in the conservative area of the gene. The resulting amplification and/or detection of the nuc region, under standard PCR conditions as described herein, demonstrates that S. aureus is present in the sample.

Oligonucleotides are as follows:

SEQ ID Oligo NO Sequence S.aureus-4 27 GGTGTAGAGAAATATGGTCCTGAAGC  primer (26 nt) S.aureus-5 28 GTCCTGAAGCAAGTGCATTTACG  primer (23 nt) S.aureus-6 29 GGACGTGGCTTAGCGTATATTTATGCTGATG  Probe (31 nt) S.aureus-7 30 GCAACTTTAGCCAAGCCTTGAC  primer (22 nt)

Example 6 Amplification of mecA and mecA Variant

Standard PCR conditions, as described above, can be utilized, unless noted differently.

mecA encodes PBP2a (Penicillin Binding Protein 2a), which is a modified PBP. mecA variant discovered recently also encodes for a protein belonging to the PBP2a family. After building a multiple sequence alignment (from a collection of sequences from proprietary and/or public databanks), the oligonucleotides were designed in conservative areas of the gene. Oligonucleotides can be designed in order to amplify and detect both mecA and mecA variant either in the same simplex reaction or in several distinct simplex reactions or in multiplex reaction. The resulting amplification and/or detection of mecA and/or mecA variant (in simplex or multiplex) demonstrate that the methicillin resistance gene is present in the sample.

mecA can be assayed by amplification using the following oligonucleotides, under standard PCR conditions:

SEQ ID Oligo NO Sequence Fwd Primer 12 ACCTTCTACACCTCCATATCAC (22 nt) mecA-1 Rev Primer 13 CGTTACGGATTGCTTCACTG (20 nt) mecA-2

mecA variant can be assayed by amplification using the following oligonucleotides to detect mecA variant sequences:

SEQ ID Oligo NO Sequence Fwd Primer 14 AACACTGATGGTTTTAAGGTATCCA  mecAv-1 (25 nt) Fwd Primer 15 AAGGTATCCATTGCAAATACTTATGACAA  mecAv-2 (29 nt) Rev Primer 16 TACCAGATCCATCGTCATTTTTCATATGT  mecAv-3 (29 nt) Rev Primer 17 TACCAGATCCATCGTCATTTTTCATAT  mecAv-4 (27 nt) Probe 18 ATTGGAGAAAAAGGCTGAAAACGGAA  mecAv-5 (26 nt) Probe 19 ATTGGAGAAAAAGGCTGAAAACGGAAAAGA  mecAv-6 (30 nt) Fwd Primer 20 CCAGATATAGTAGCATTATA (20 nt) mecAv-7 Rev Primer  21 AAAGATGACGATATTGAG (18 nt) Probe mecAv-8

Alternatively, mecA variant can be determined using a mecA variant-orfX assay. One such assay is exemplified above in Example 2.

An assay to detect both mecA and mecA variant is described below. Primer/probe sequences are selected in a region common to both mecA and mecA variant.

mecA+mecA variant can be amplified using the following oligonucleotides:

SEQ ID Oligo NO Sequence Primer 22 TCACCAGGTTCAACYCAAAA  mecA-mecAv-1 (20 nt) Primer 23 CCTGAATCWGCTAATAATATTTC  mecA-mecAv-2 (23 nt)

All patents, patent publications and non-patent publications cited herein and the material for which they are cited are specifically incorporated by reference herein. Nothing herein is to be construed as an admission that the invention is not entitled to antedate such disclosure by virtue of prior invention.

It is understood that the disclosed invention is not limited to the particular methodology, protocols, and reagents described as these may vary. It is also to be understood that the terminology used herein is for the purpose of describing particular embodiments only, and is not intended to limit the scope of the present invention which will be limited only by the appended claims.

Those skilled in the art will recognize, or be able to ascertain using no more than routine experimentation, many equivalents to the specific embodiments of the invention described herein. Such equivalents are intended to be encompassed by the following claims.

Sequences

Oligo- SEQ nucleo- ID tide NO Target Sequence mecAv-  1 MecA ATGAAGCAATATCAAAGGA (19 nt) orfX-1 variant- orfX mecAv-  2 MecA TGAAGCAATATCAAAGGAA (19 nt) orfX-2 variant- orfX mecAv-  3 MecA ATAACTTGGTTATTCAAAGATGACGATATT orfX-3 variant- (30 nt) orfX mecAv-  4 MecA ACTTGGTTATTCAAAGATGACGATATTGA orfX-4 variant- (29 nt) orfX mecAv-  5 MecA TGGTTATTCAAAGATGACGATATTGAGA orfX-5 variant- (28 nt) orfX mecAv-  6 MecA ATCCTAATATGTTAATGGCGA (21 nt) orfX-6 variant- orfX mecAv-  7 MecA ATGGCGATTAATGTTAAAGA (20 nt) orfX-7 variant- orfX mecAv-  8 MecA TGGCCAGCTATAATGCTACTATATCTGGA orfX-8 variant- (29 nt) orfX mecAv-  9 MecA TCAGCAAAATGACATTTCCACATCA orfX-9 variant- (25 nt) orfX mecAv- 10 MecA TCAGCAAAATGACATTCCCACATCA orfX-10 variant- (25 nt) orfX mecAv- 11 MecA TGATGCGGGTTGTGTTAATTGARCAAGTG orfX-11 variant- (29 nt) orfX mecA-1 12 mecA ACCTTCTACACCTCCATATCAC (22 nt) mecA-2 13 mecA CGTTACGGATTGCTTCACTG (20 nt) mecAv-1 14 mecA AACACTGATGGTTTTAAGGTATCCA variant (25 nt) mecAv-2 15 mecA AAGGTATCCATTGCAAATACTTATGACAA variant (29 nt) mecAv-3 16 mecA TACCAGATCCATCGTCATTTTTCATATGT variant (29 nt) mecAv-4 17 mecA TACCAGATCCATCGTCATTTTTCATAT variant (27 nt) mecAv-5 18 mecA ATTGGAGAAAAAGGCTGAAAACGGAA variant (26 nt) mecAv-6 19 mecA ATTGGAGAAAAAGGCTGAAAACGGAAAAGA variant (30 nt) mecAv-7 20 mecA CCAGATATAGTAGCATTATA (20 nt) variant mecAv-8 21 mecA AAAGATGACGATATTGAG (18 nt) variant mecA- 22 mecA + TCACCAGGTTCAACYCAAAA (20 nt) mecAv-1 mecA variant mecA- 23 mecA + CCTGAATCWGCTAATAATATTTC mecAv-2 mecA (23 nt) variant S. 24 spa CACCTGCTGCAAATGCTG (18 nt) aureus-1 S. 25 spa CGTTGATCAGCRTTTAAGTTAGGCATATT aureus-2 (29 nt) S. 26 spa CGCAACACGATGAAGCTCAACAAAATGC aureus-3 (28 nt) S. 27 nuc GGTGTAGAGAAATATGGTCCTGAAGC aureus-4 (26 nt) S. 28 nuc GTCCTGAAGCAAGTGCATTTACG aureus-5 (23 nt) S. 29 nuc GGACGTGGCTTAGCGTATATTTATGCTGATG aureus-6 (31 nt) S. 30 nuc GCAACTTTAGCCAAGCCTTGAC (22 nt) aureus-7 

What is claimed is:
 1. A method of amplifying in a sample a methicillin-resistant Staphylococcus aureus (MRSA) which comprises an insertion of a SCCmec cassette within Staphylococcus aureus chromosomal DNA, wherein the SCCmec cassette comprises a mecA variant element, the method comprising: performing on the sample an amplification reaction utilizing an oligonucleotide set consisting of: a. a first oligonucleotide having a nucleic acid sequence that specifically hybridizes to chromosomal Staphylococcus aureus DNA in an extremity junction region, and b. a second oligonucleotide having a nucleic acid sequence that specifically hybridizes to a mecA variant, wherein each of the first oligonucleotide and the second oligonucleotide is oriented such that, under amplification conditions, if the sample contains the MRSA, the region of the MRSA between the hybridizing site of the first oligonucleotide and the hybridizing site of the second oligonucleotide is amplified as a single amplicon.
 2. The method of claim 1, wherein the extremity junction region of chromosomal S. aureus DNA is a right extremity junction region.
 3. The method of claim 1, wherein the amplification reaction further comprises a third oligonucleotide that specifically hybridizes within a region of the MRSA between the hybridizing site of the first oligonucleotide and the hybridizing site of the second oligonucleotide, and wherein if the sample contains the MRSA, hybridization of the third oligonucleotide is detected.
 4. The method of claim 1, further comprising contacting the amplified sample with an intercalating dye, wherein if the sample contains the MRSA, intercalation of the dye into an amplification product is detected.
 5. The method of claim 3, wherein the third oligonucleotide specifically hybridizes to chromosomal Staphylococcus aureus DNA.
 6. The method of claim 3, wherein the third oligonucleotide specifically hybridizes to orfX of chromosomal Staphylococcus aureus DNA.
 7. The method of claim 3, wherein the third oligonucleotide specifically hybridizes to a right extremity junction region of SCCmec cassette DNA.
 8. The method of claim 3, wherein the third oligonucleotide specifically hybridizes to the mecA variant.
 9. The method of claim 1, wherein the first oligonucleotide specifically hybridizes to orfX of chromosomal Staphylococcus aureus DNA.
 10. The method of claim 1, wherein the mecA variant is mecA_(LGA251).
 11. The method of claim 1, wherein the first oligonucleotide comprises a nucleic acid sequence selected from the group consisting of SEQ ID NO: 9 and SEQ ID NO:
 10. 12. The method of claim 1, wherein the second oligonucleotide comprises a nucleic acid sequence selected from the group consisting of SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO:14, SEQ ID NO:15, SEQ ID NO:16, SEQ ID NO:17, SEQ ID NO:20 and SEQ ID NO:21.
 13. The method of claim 3, wherein the third oligonucleotide comprises a nucleic acid sequence selected from the group consisting of SEQ ID NO:8, SEQ ID NO:11, SEQ ID NO:18 and SEQ ID NO:19.
 14. The method of claim 1, further comprising amplifying a methicillin-resistant Staphylococcus aureus (MRSA) which comprises an insertion of a SCCmec cassette within Staphylococcus aureus chromosomal DNA, wherein the SCCmec cassette comprises a mecA, by utilizing in an amplification reaction a second oligonucleotide set for amplification of a right extremity junction of SCCmec cassette with Staphylococcus aureus chromosomal DNA, the second oligonucleotide set comprising: a. a first junction oligonucleotide having a nucleic acid sequence that specifically hybridizes within chromosomal Staphylococcus aureus DNA in a right extremity junction region; and b. a second junction oligonucleotide having a nucleic acid sequence that specifically hybridizes within a right extremity junction region of the SCCmec cassette of the MRSA comprising a mecA, wherein each of the first junction oligonucleotide and the second junction oligonucleotide is oriented such that, under amplification conditions, if the sample contains the MRSA comprising a mecA, the right extremity junction is amplified.
 15. The method of claim 14, wherein the amplification reaction further comprises a third junction oligonucleotide having a nucleic acid sequence that specifically hybridizes within a region of the MRSA between the hybridizing site of the first junction oligonucleotide and the hybridizing site of the second junction oligonucleotide, wherein if the sample contains the MRSA comprising the right extremity junction, hybridization of the third junction oligonucleotide is detected.
 16. The method of claim 15, wherein the third junction oligonucleotide has a nucleic acid sequence that specifically hybridizes within a right extremity junction region of the SCCmec cassette.
 17. The method of claim 15, wherein the third junction oligonucleotide has a nucleic acid sequence that specifically hybridizes within orfX.
 18. The method of claim 15, wherein the first oligonucleotide has a nucleic acid sequence that specifically hybridizes within orfX.
 19. The method of claim 1, further comprising amplifying a Staphylococcus aureus comprising mecA by utilizing in an amplification reaction a third oligonucleotide set for amplification of a mecA element consisting of: a. a first mecA oligonucleotide having a nucleic acid sequence that specifically hybridizes within mecA DNA; and b. a second mecA oligonucleotide having a nucleic acid sequence that specifically hybridizes within mecA DNA, wherein each of the first mecA oligonucleotide and the second mecA oligonucleotide is oriented such that, under amplification conditions, a portion of the mecA DNA is amplified.
 20. The method of claim 19, wherein the amplification reaction further comprises a third mecA oligonucleotide having a nucleic acid sequence that specifically hybridizes within a region of the mecA between the hybridizing site of the first mecA oligonucleotide and the hybridizing site of the second mecA oligonucleotide, wherein if the sample contains the MRSA comprising mecA, hybridization of the third mecA oligonucleotide is detected.
 21. The method of claim 1, further comprising utilizing a fourth oligonucleotide set for amplification of a Staphylococcus aureus-specific chromosomal DNA, the fourth oligonucleotide set consisting of: a. a first S. aureus oligonucleotide having a nucleic acid sequence that specifically hybridizes within Staphylococcus aureus-specific chromosomal DNA; and b. a second S. aureus oligonucleotide having a nucleic acid sequence that specifically hybridizes within Staphylococcus aureus-specific chromosomal DNA, wherein each of the first S. aureus oligonucleotide and the second S. aureus oligonucleotide is oriented such that, under amplification conditions, a portion of the S. aureus-specific DNA is amplified.
 22. The method of claim 21, wherein the amplification reaction further comprises a third S. aureus oligonucleotide having a nucleic acid sequence that specifically hybridizes within the S. aureus DNA between the hybridizing site of the first S. aureus oligonucleotide and the hybridizing site of the second S. aureus oligonucleotide, wherein if the sample contains the region of the S. aureus DNA between the hybridizing site of the first S. aureus oligonucleotide and the hybridizing site of the second S. aureus oligonucleotide, hybridization of the third oligonucleotide is detected.
 23. The method of claim 21, wherein the Staphylococcus aureus-specific chromosomal DNA is selected from the group consisting of spa, orfX and nuc.
 24. A method of amplifying in a sample a methicillin-resistant Staphylococcus aureus (MRSA) which comprises an insertion of a SCCmec cassette within Staphylococcus aureus chromosomal DNA, wherein the SCCmec cassette comprises mecA or a mecA variant element, the method comprising: performing on the sample an amplification reaction utilizing a. a first oligonucleotide set consisting of: 1) a first mecA variant oligonucleotide having a nucleic acid sequence that specifically hybridizes to a mecA variant element, and 2) a second mecA variant oligonucleotide having a nucleic acid sequence that specifically hybridizes to a mecA variant element; and b. a second oligonucleotide set consisting of: 1) a first mecA oligonucleotide having a nucleic acid sequence that specifically hybridizes to mecA, and 2) a second mecA oligonucleotide having a nucleic acid sequence that specifically hybridizes to mecA, wherein each of the first oligonucleotide and the second oligonucleotide is oriented such that, under amplification conditions, if the sample contains the MRSA, the region of the MRSA between the hybridizing site of the first oligonucleotide and the hybridizing site of the second oligonucleotide is amplified.
 25. The method of claim 24, wherein the amplification reaction further comprises a third mecA variant oligonucleotide that specifically hybridizes within a region of the MRSA between the hybridizing site of the first mecA variant oligonucleotide and the hybridizing site of the second mecA variant oligonucleotide, and wherein if the sample contains the MRSA comprising a mecA variant element, hybridization of the third mecA variant oligonucleotide is detected.
 26. The method of claim 24, wherein the amplification reaction further comprises a third mecA oligonucleotide that specifically hybridizes within a region of the MRSA between the hybridizing site of the first mecA oligonucleotide and the hybridizing site of the second mecA oligonucleotide, and wherein if the sample contains the MRSA comprising mecA, hybridization of the third mecA oligonucleotide is detected.
 27. The method of claim 24, further comprising contacting the amplified sample with an intercalating dye, wherein if the sample contains the MRSA, intercalation of the dye into an amplification product is detected.
 28. The method of claim 24, wherein the first mecA variant oligonucleotide comprises a nucleic acid sequence selected from the group consisting of SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO:14, SEQ ID NO:15 and SEQ ID NO:20.
 29. The method of claim 24, wherein the second mecA variant oligonucleotide comprises a nucleic acid sequence selected from the group consisting of SEQ ID NO:16, SEQ ID NO:17 and SEQ ID NO:
 21. 30. The method of claim 25, wherein the third mecA variant oligonucleotide comprises a nucleic acid sequence selected from the group consisting of SEQ ID NO:8, SEQ ID NO:18 and SEQ ID NO:
 19. 31. The method of claim 1, wherein the mecA variant is meCA_(LGA251).
 32. The method of claim 24, further comprising amplifying a methicillin-resistant Staphylococcus aureus (MRSA) which comprises an insertion of an SCCmec cassette within Staphylococcus aureus chromosomal DNA, wherein the SCCmec cassette comprises a mecA, by utilizing in an amplification reaction a second oligonucleotide set for amplification of a right extremity junction of SCCmec cassette with Staphylococcus aureus chromosomal DNA, the second oligonucleotide set comprising: a. a first junction oligonucleotide having a nucleic acid sequence that specifically hybridizes within chromosomal Staphylococcus aureus DNA in a right extremity junction region; and b. a second junction oligonucleotide having a nucleic acid sequence that specifically hybridizes within a right extremity junction region of the SCCmec cassette of the MRSA comprising a mecA, wherein each of the first junction oligonucleotide and the second junction oligonucleotide is oriented such that, under amplification conditions, if the sample contains the MRSA comprising a mecA, the right junction is amplified.
 33. The method of claim 32, wherein the amplification reaction further comprises a third junction oligonucleotide having a nucleic acid sequence that specifically hybridizes within a region of the MRSA between the hybridizing site of the first junction oligonucleotide and the hybridizing site of the second junction oligonucleotide, wherein if the sample contains the MRSA comprising the right extremity junction, hybridization of the third junction oligonucleotide is detected.
 34. The method of claim 32, wherein the third junction oligonucleotide has a nucleic acid sequence that specifically hybridizes within a right extremity junction region of the SCCmec cassette.
 35. The method of claim 32, wherein the first junction oligonucleotide has a nucleic acid sequence that specifically hybridizes within orfX.
 36. The method of claim 32, wherein the third junction oligonucleotide has a nucleic acid sequence that specifically hybridizes within orfX.
 37. The method of claim 24, further comprising utilizing a fourth oligonucleotide set for amplification of a Staphylococcus aureus-specific chromosomal DNA, the fourth oligonucleotide set consisting of: a. a first S. aureus oligonucleotide having a nucleic acid sequence that specifically hybridizes within Staphylococcus aureus-specific chromosomal DNA; and b. a second S. aureus oligonucleotide having a nucleic acid sequence that specifically hybridizes within Staphylococcus aureus-specific chromosomal DNA, wherein each of the first S. aureus oligonucleotide and the second S. aureus oligonucleotide is oriented such that, under amplification conditions, a portion of the S. aureus-specific DNA is amplified.
 38. The method of claim 37, wherein the amplification reaction further comprises a third S. aureus oligonucleotide having a nucleic acid sequence that specifically hybridizes within the S. aureus DNA between the hybridizing site of the first S. aureus oligonucleotide and the hybridizing site of the second S. aureus oligonucleotide, wherein if the sample contains the of the S. aureus DNA between the hybridizing site of the first S. aureus oligonucleotide and the hybridizing site of the second S. aureus oligonucleotide, hybridization of the third oligonucleotide is detected.
 39. The method of claim 37, wherein the Staphylococcus aureus-specific chromosomal DNA is selected from the group consisting of spa, orfX and nuc. 